SPMology
An hypertextual digest of the SPM, FSL, MRIcro, and pyMVPA2 archives
SPM@JISCMAIL.AC.UK https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=spm
FSL@JISCMAIL.AC.UK https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=fsl
MRICRO@JISCMAIL.AC.UK https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=MRICRO
PKG-EXPPSY-PYMVPA@LISTS.ALIOTH.DEBIAN.ORG http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/
Index
Image format conversion & modifications
Statistics for event-related designs
Statistical Nonparametric Mapping (SnPM)
Psycho-Physiological Interactions
SPM function, Toolboxes & Miscellaneous
1a) How do you trace back old http links to the SPM archives?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=SPM&P=R450416&I=-3
Date: Fri, 19 Aug 2005 23:44:53 +0100 From: "Stephen J. Fromm" Subject: Retrieving broken links in posts: solution
2a) How do you cancel out scanner noise from vocal recordings?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=spm&O=D&F=&S=&P=17435
Date: Thu, 11 Jan 2007 09:22:55 -0500 From: Peter LaViolette Subject: Re: Repost: Paradigm with scan pauses http://www.mrc-cbu.cam.ac.uk/~rhodri/scannernoisecancellation/
2b) How do you reduce signal loss in fMRI EPI acquisitions?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=spm&O=D&F=&S=&P=24579
Date: Mon, 14 Apr 2008 17:52:47 +0200 From: "Neggers, S.F.W." Subject: Re: Which software can solve the problem of susceptibility-induced signal losses in EPI images
2c) How do you measure Signal to Noise ratio?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0503&L=spm&O=D&F=&S=&P=42753
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0506&L=spm&O=D&F=&S=&P=10384
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0506&L=spm&O=D&F=&S=&P=10699
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0506&L=spm&O=D&F=&S=&P=11652
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0506&L=spm&O=D&F=&S=&P=11754
2d) How do you measure SNR on normalized images?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901&L=SPM&D=1&T=0&O=D&P=48669
Subject: Re: Several ways to compute the SNR From: Christian Gaser Date: Fri, 9 Jan 2009 07:39:59 +0000
2e) How do you optimize a field map acquisition?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0906&L=SPM&D=1&T=0&O=D&P=75227
Subject: Re: On the optimum settings for B0 fieldmaps From: Chloe Hutton Date: Mon, 8 Jun 2009 16:41:46 +0100
2f) How do you best acquire fMRI data (continuous vs. interleaved)?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0907&L=SPM&D=1&T=0&O=D&P=36644
Subject: Re: DCM - interleaved sequence From: Klaas Enno Stephan Date: Mon, 6 Jul 2009 16:49:51 +0000
2g) How do you avoid y-direction drift during EPI acqusitions on Philips scanners?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1001&L=SPM&T=0&O=D&P=10719
Subject: Re: Abnormal Realignment Result?? From: "Neggers, S.F.W." Date: Mon, 4 Jan 2010 11:48:48 +0100
2h) Do you include gaps between slices in voxel dimensions?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1009&L=SPM&D=0&P=191704
Subject: Re: how SPM treats gap between slices? From: John Ashburner Date: Mon, 27 Sep 2010 09:34:56 +0100
2i) Considerations of inter-trial intervals and jittered SOAs:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1110&L=SPM&F=&S=&P=209808
Subject:Re: Questions about ER design timing From:Rik Henson Date:Tue, 11 Oct 2011 08:57:08 +0000
2j) Is fieldmap undistortion required for data acquired on a Philips Achieva? → No
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;b67ea103.1112
Subject:Re: FieldMap Toolbox with Philips Achieva data From:Richard Morris Date:Mon, 12 Dec 2011 11:33:36 +0000
2k) How do you optimize the choice of both TE for the acquisition of a fieldmap?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1203&L=spm&D=0&P=95281
Subject:Re: acquiring fieldmaps - which TE to use? From:Michael Harms Date:Mon, 5 Mar 2012 22:04:36 -0600
2i) What is the current (as of 2012) PET temporal resolution?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1212&L=spm&F=&S=&P=11474
Subject: Re: current PET time resolution From: Alexander Hammers Date: Sun, 2 Dec 2012 20:22:20 +0100
3. Image format conversion & modifications
3a) Is it better to export PAR/REC or DICOM files on a Philips Scanner?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0801&L=mricro&T=0&F=&S=&P=168
Date: Wed, 2 Jan 2008 23:40:17 +0000 From: Chris Rorden Subject: Re: dcm2nii with Philips and rescale slope value
3b) How do you convert fieldmap Philips images with MriCro?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0802&L=mricro&T=0&F=&S=&P=1413
Date: Wed, 27 Feb 2008 22:20:21 +0000 From: Chris Rorden Subject: Re: dcm2nii problems with philips achieva
3c) How do you convert an Analyze file into a Nifti file?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&O=D&P=359772
Date: Fri, 23 Sep 2005 12:11:41 -0400 From: Rich Hammett Subject: Re: NIfTI single-file (.nii) option in SPM5b ??? In AFNI: head -c 4 /dev/zero > 4bytes cat f.hdr 4bytes f.img > f.nii
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&T=0&O=D&P=446110
Date: Mon, 4 Dec 2006 17:56:59 -0600 From: Darren G Subject: Re: .nii files
3d) How do you convert a Nifti file into an Analyze file?
with MRICro (Convert nii to img+hdr pair)
with FSL: fslchfiletype ANALYZE myimage_brain.nii.gz
or:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0711&L=spm&O=D&F=&S=&P=877
Date: Thu, 1 Nov 2007 09:27:53 -0700 From: Russell Poldrack Subject: Re: Convert nii to Analyze 7.5
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0711&L=spm&O=D&F=&S=&P=1134
Date: Thu, 1 Nov 2007 13:36:31 -0400 From: Mikolaj Pawlak Subject: Re: Convert nii to Analyze 7.5
3e) How do you modify a header parameter (e.g. voxel size) in SPM2?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0608&L=spm&O=D&P=42299
Date: Fri, 25 Aug 2006 11:19:42 +0100 From: John Ashburner Subject: Re: Analyze Header Voxel Size
3f) How do you read header information (e.g. Handedness) from NIFTI files?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0811&L=spm&D=1&T=0&O=D&P=7264
Subject: Re: Q: Command to tell whether a Nifti image actually contains L-R info within it? From: John Ashburner Date: Thu, 6 Nov 2008 13:00:58 +0100
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0811&L=spm&D=1&T=0&O=D&P=6382
Subject: Re: Q: Command to tell whether a Nifti image actually contains L-R info within it? From: Kathy Pearson Date: Wed, 5 Nov 2008 17:35:36 -0600
3g) Problems with EEG Neuroscan data conversion in SPM8:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=SPM&D=1&T=0&O=D&P=228566
Subject: Re: Neuroscan 32 bits data convert to spm8 data From: Vladimir Litvak Date: Sat, 25 Apr 2009 15:04:03 +0100
3h) Note on dcm2nii conversion of Philips DTI files?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=MRICRO;89144089.1503
Subject: Re: x-files? From: Chris Rorden Date: Sun, 8 Mar 2015 18:33:55 +0000
3i) How do you reset image orientation and modify header parameters in SPM12?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1606&L=spm&F=&S=&P=620580
Subject:Re: Modifying headers without reading the whole image volume From:Guillaume Flandin Date:Tue, 21 Jun 2016 13:21:12 +0100
4a) What is the standard preprocessing procedure in SPM5?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=spm&O=D&F=&S=&P=11612
Date: Tue, 9 Jan 2007 15:33:00 +0100 From: "Ashburner John (PSYCHOLOGY)" Subject: Re: manual
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=spm&O=D&F=&S=&P=10945
Date: Tue, 9 Jan 2007 13:05:43 +0100 From: "Simon B. Eickhoff" Subject: Re: manual (preprocessing)
4b) How do you verify the order of slice acquisition within your fMRI volumes?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=6151362
Date: Tue, 28 Nov 2006 22:28:08 -0600 From: Darren Gitelman Subject: Re: Slice time correction: SPM5
4c) How do you specify microtime onset for slice timed interleaved fMRI sequences?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0706&L=spm&F=&S=&P=531640
Date: Fri, 29 Jun 2007 12:23:10 +0100 From: Rik Henson Subject: Re: Interleaved acquisition and microtime specification
4d) How do you compile the FieldMap Toolbox for SPM5?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0611&L=spm&O=D&P=6627
Date: Mon, 6 Nov 2006 18:24:06 +0000 From: Paul Macey Subject: Re: Fieldmap-generation in spm5
4e) When and how do I perform Unwarp & Realign?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=spm&O=D&P=244252
Date: Fri, 16 Jul 2004 10:36:39 +0200 From: Jesper Andersson Subject: Re: Realign & Unwarp (+/- motion parameters)
4f) How do you use magnitude/phase image pairs in the Fieldmap Toolbox?
In SPM5 this is obsolete! see /mnt/hda5/work/spm/FieldMap_protocol_3apr07.txt
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=SPM&P=R73895&I=-3
Date: Fri, 5 Mar 2004 12:57:36 +0100 From: Andreas Bartsch Subject: Re: Unwarping toolbox
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=SPM&P=R76021&I=-3
Date: Mon, 8 Mar 2004 11:43:48 +0000 From: Chloe Hutton Subject: Re: Unwarping toolbox
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=SPM&P=R75876&I=-3
Date: Mon, 8 Mar 2004 12:43:51 +0200 From: Jesper Andersson Subject: Re: Unwarping toolbox
4g) How do you adjust a pre-calculated fieldmap in the -pi +pi radians range?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0711&L=spm&O=D&F=&S=&P=1552
Date: Thu, 1 Nov 2007 12:39:05 -0700 From: Paul Macey Subject: Re: Field map toolbox in SPM5
4h) When do I perform wrapping during realignment?
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind04&L=SPM&P=R469452&I=-3
4i) How much motion is too much? How do you detect residual motion-related variance?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&O=D&P=291490
From: Russ Poldrack Subject: Re: How much motion is too much?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&O=D&P=293378
From: Darren Gitelman Subject: Re: How much motion is too much?
tsdiffana.m
http://imaging.mrc-cbu.cam.ac.uk/imaging/DataDiagnostics
see also: http://www.mrc-cbu.cam.ac.uk/~jessica/Imageanalysis3test.htm
Intersting post on MANCOVA and spm_cva:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1403&L=spm&F=&S=&P=756559
Subject:Re: How much head motion From:John Ashburner Date:Thu, 27 Mar 2014 20:21:23 +0000
4j) How do you deal with bad volumes?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&O=D&P=421566
Date: Thu, 10 Nov 2005 00:19:13 +0100 From: Karsten Specht Subject: Re: Deleting bad volumes
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&O=D&P=421673
Date: Wed, 9 Nov 2005 18:59:40 -0500 From: Joern Diedrichsen Subject: Re: Deleting bad volumes
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&O=D&F=&S=&P=375182
Date: Mon, 9 Oct 2006 12:13:08 +0100 From: Helmut Laufs Subject: Re: Motion during task
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&O=D&F=&S=&P=375499
Date: Mon, 9 Oct 2006 22:49:20 +0100 From: Paul Mazaika Subject: Re: Motion during task
more...
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0807&L=spm&T=0&O=D&P=43491
Subject: Re: removing unwanted fMRI volumes
From: Paul Mazaika
Date:Thu, 31 Jul 2008 18:53:54 +0100
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0808&L=spm&T=0&O=D&P=472
Subject: Re: removing unwanted fMRI volumes
From: "Stephen J. Fromm"
Date:Fri, 1 Aug 2008 12:57:56 +0100
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0808&L=spm&T=0&O=D&P=1167
Subject: Re: removing unwanted fMRI volumes
From: Daniel Kimberg
Date:Fri, 1 Aug 2008 17:55:47 +0100
still more...
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=SPM&D=1&T=0&O=D&P=16201
Subject: Re: modelling out task related movement From: Paul Mazaika Date: Wed, 1 Apr 2009 14:55:09 -0700
important note!!
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=spm&F=&S=&P=978667
Subject: Re: include motion parameters only for some subjects? From: Darren Gitelman Date: Thu, 30 Apr 2009 17:21:38 -0500
4k) How do you deal with subjects with high movements (e.g. children)?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&O=D&F=&S=&P=380677
http://cibsr.stanford.edu/tools/ArtRepair.htm Date: Sat, 14 Oct 2006 00:07:40 +0100 From: Paul Mazaika Subject: New software for high motion clinical subjects
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&O=D&F=&S=&P=400050
http://www.bangor.ac.uk/~pss412/imaging/robustWLS.html
Date: Thu, 26 Oct 2006 10:27:00 +0100 From: Joern Diedrichsen Subject: Re: Motion during task
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;ed996e94.1511
Subject: Re: Artrepair and Motion Regressors From:"Carmichael, David" Date:Wed, 4 Nov 2015 16:40:04 +0000
4l) How do you remove artifactual components from time series and/or design matrices?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&O=D&F=&S=&P=285174
Date: Fri, 11 Aug 2006 08:48:35 -0400 From: "Vince D. Calhoun" Subject: Re: Filtering of periodic noise
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&O=D&F=&S=&P=285290
Date: Fri, 11 Aug 2006 09:13:17 -0400 From: Eric Zarahn Subject: Re: Filtering of periodic noise
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&O=D&F=&S=&P=286132
Date: Fri, 11 Aug 2006 12:12:22 -0400 From: "Vince D. Calhoun" Subject: Re: Filtering of periodic noise
4m) How do you remove coloured noise artifacts (contributions from cardiac pulsation and respiration), particularly in the ventricles?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=spm&O=D&F=&S=&P=4391
Date: Mon, 5 May 2008 21:13:13 +0200 From: Torben Ellegaard Lund Subject: Re: Activations in CSF/ventricles?
4n) How do you repair images with stripes due to motion artifacts for an interleaved scan sequence?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=spm&O=D&F=&S=&P=605
Date: Tue, 2 Jan 2007 18:25:19 +0000
From: Paul Mazaika
Subject: Re: Anyone who have experience to judge whether this "activation"
is real BOLD or head motion?
4o) How do you display the coefficients of the cosine basis of image normalization?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0412&L=spm&O=D&F=&S=&P=1166
4p) How do I perform spatial normalization of lesioned brains in SPM2?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0501&L=spm&O=D&F=&S=&P=33880
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0912&L=MRICRO&D=1&T=0&O=D&P=8850
Subject: Re: Lesion analysis From: Chris Rorden Date: Thu, 31 Dec 2009 13:30:18 +0000
4q) Is it better to perform segmentation in 2 step (second time on bias corrected images)?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=SPM&P=R33088&I=-3
Date: Thu, 12 Jan 2006 12:30:38 +0100 From: John Ashburner Subject: Re: unified segmentation and bias correction - two steps?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=SPM&P=R31539&I=-3
Date: Wed, 11 Jan 2006 18:01:59 -0600 From: Darren Gitelman Subject: Re: unified segmentation and bias correction - two steps?
4r) How can the SPM5 segmentation/normalization of EPI scans be improved?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0807&L=spm&F=&S=&P=314428
Date: Thu, 10 Jul 2008 11:53:43 +0100 From: John Ashburner Subject: Re: individual functional and anatomical superimposition
and:
Subject: Re: SPM5's normalization procedure From: John Ashburner Date: Tue, 30 Sep 2008 15:26:35 +0100
and related issue:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;b869f419.1203
Subject: Re: Normalization of EPI using unified segmentation From:"Neggers, S.F.W." Date:Tue, 13 Mar 2012 11:31:19 +0000
4s) How do you best perform nonlinear registration / normalisation / warping?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709&L=spm&O=D&F=&S=&P=27526
Date: Wed, 26 Sep 2007 11:51:45 +0100 From: John Ashburner Subject: Re: Sir Need your suggestion
see also HAMMER
https://www.rad.upenn.edu/sbia/software/index.html#hammer
4t) Improved normalisation algorithms in newer SPM versions (VBM approach, DARTEL and others):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0803&L=spm&F=&S=&P=408457
Date: Mon, 31 Mar 2008 13:40:56 +0000 From: John Ashburner Subject: Re: RAVENS maps vs SPM5 modulated data in VBM: Question on smoothness
in spm8:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=spm&F=&S=&P=563051
Subject: Re: Writing normalised images with new segment From: John Ashburner Date: Thu, 21 May 2009 12:09:51 +0000
4u) How do you apply normalization parameters and maintain the bounding box and voxel size of the original image?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0809&L=SPM&T=0&F=&S=&P=96029
Subject: Re: Warping ROIs From: John Ashburner Date: Tue, 16 Sep 2008 18:31:55 +0100
4v) Where do you obtain a GM and WM DARTEL average template of 471 healthy subjects?
http://www.fil.ion.ucl.ac.uk/~john/misc/ http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=spm&O=D&F=&S=&P=22884 Date: Fri, 16 May 2008 11:37:25 +0000 From: John Ashburner Subject: Re: Dartel template
4w) How do you create a custom population-matched pediatric template?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=spm&O=D&F=&S=&P=3069
Date: Wed, 2 Apr 2008 17:51:17 +0200 From: Marko Wilke Subject: Announcing the Template-O-Matic toolbox for creating custom pediatric templates
http://dbm.neuro.uni-jena.de/software/tom/
4x) Are 4D fMRI files supported in SPM5?
yes, but....
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=spm&O=D&F=&S=&P=28938
Date: Thu, 25 Oct 2007 12:59:58 +0100 From: John Ashburner Subject: Re: 4D-support broken? was: [SPM] 5D NIfTI files, @nifti class
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=spm&O=D&F=&S=&P=29829
Date: Thu, 25 Oct 2007 15:38:51 +0200 From: Roland Marcus Rutschmann Subject: Re: 4D-support broken? was: [SPM] 5D NIfTI files, @nifti class
4y) How do you apply skull stripping to improve normalisation?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0812&L=spm&D=1&T=0&O=D&P=962
Subject: Re: wrong normalize From: John Ashburner Date: Mon, 1 Dec 2008 14:37:21 +0100
4z) How do you visualize time-series in a movie to check image alignment using matlab?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=SPM&D=1&T=0&O=D&P=182842
Subject: Re: Check realignment and normalization video clip From: Cyril Pernet Date: Thu, 21 May 2009 07:57:10 +0100
or: spm_movie.m (in add_ons)
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=spm&F=&S=&P=571370
Subject: Re: Check realignment and normalization video clip From: John Ashburner Date: Thu, 21 May 2009 12:53:21 +0000
4a1) Complicated work-around for normalizing (truncated) EPI images with SPM8 and DARTEL:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0909&L=SPM&T=0&O=D&P=8666
Subject: AW: [SPM] SPM8: DARTEL normalise to MNI problem with partial coverage EPIs From: Christian Büchel Date: Tue, 1 Sep 2009 16:07:26 +0200
4b1) Improvements in SPM8 New Segmentation over previous Segmentation alorithms?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=SPM&D=1&T=0&O=D&P=160606
Subject: Re: New segmentation vs Segment (SPM8) From: John Ashburner Date: Fri, 12 Feb 2010 15:33:19 +0000
4b2) Improvements in SPM12 Segmentation over previous Segmentation alorithms?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1412&L=spm&F=&S=&P=238181
Subject:Re: The m-file corresponding to Segment button in SPM8 or SPM12 From:John Ashburner Date:Mon, 8 Dec 2014 11:28:36 +0000
4c1) Objective metrics to evaluate the quality of normalisation:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1003&L=spm&F=&S=&P=841853
Subject: Re: Is there an objective, ideally quantitative, way to tell if normalization is "not good enough"? From: cyril pernet Date: Mon, 29 Mar 2010 10:52:36 +0100
see also:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1111&L=spm&F=&S=&P=87676
Subject:Re: Which is better normalization method From:John Ashburner Date:Fri, 4 Nov 2011 11:52:41 +0000
4d1) Create template for longitudinal study:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1201&L=spm&F=&S=&P=203694
Subject: Re: DARTEL template from baseline scan, applied to other timepoints From: John Ashburner Date: Wed, 11 Jan 2012 19:06:58 +0000
4e1) How to visualize the deformations of spatial normalisation on an image grid:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;30d96ef0.1212
Subject:Re: Visualize normalization matrix? From:"Dorian P." Date:Tue, 18 Dec 2012 11:20:37 -0500
4f1) Slice timing for Multi-Band sequences:
Use SPM12 (but code provided by G. Flandin may be compatible with SPM8 as well)
Subject: Re: slice timing correction for multiband sequences From: gj Date: Fri, 13 Oct 2017 22:35:23 +0100
Subject: Re: Multiband Slice timing From: Torben Lund Date: Wed, 6 Sep 2017 16:14:27 +0200
Subject: Re: Multiband Slice timing From: Guillaume Flandin Date: Tue, 10 Feb 2015 14:04:10 +0000
5a) How do you choose the best statistical model?
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind9911&L=spm&P=R208&I=3
5b) How do you include motion parameters as effects of no interest?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0502&L=spm&O=D&F=&S=&P=25538
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0510&L=spm&O=D&F=&S=&P=3563
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0510&L=spm&O=D&F=&S=&P=4565
5c) When do you use global scaling?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&F=&S=&P=1841704
Subject:Re: Global Scaling
From:Karl Friston
Date:Mon, 21 Mar 2005 11:53:33 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&F=&S=&P=1922531
Subject:Re: Global Scaling
From:"Kent A. Kiehl"
Date:Wed, 23 Mar 2005 00:06:16 -0500
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&F=&S=&P=1943729
Subject: Re: Global Scaling
From: Karl Friston
Date: Wed, 23 Mar 2005 14:03:52 +0000
5d) In which cases should global scaling be avoided?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=SPM&P=R62901&I=-3
Date: Mon, 23 Feb 2004 22:08:05 +0000 From: Klaas Enno Stephan Subject: Re: DCM and negative modulation - followup
http://www-psych.stanford.edu/~kalina/SPM99/Tools/rd_global.html
5e) Can you enter categorical variables as parametric modulators?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=105730
Subject:Re: SPM5 parametric modulation of event-related fMRI From:Rik Henson Date:Sat, 7 Jan 2006 15:30:28 -0000
5f) How do you set up a design with nonlinear parametric modulation?
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind00&L=spm&P=R153284&I=-1
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind00&L=spm&P=R146180&I=-1
5g) How are the regressors entered in parametric modulation scaled in SPM2?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0503&L=spm&O=D&F=&S=&P=20771
5h) How do you specify SOAs with respect to the reference slice choosen in slice timing?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=spm&F=&S=&P=5211486
Date: Fri, 1 Oct 2004 13:29:56 +0100
From: Rik Henson
Subject: Re: slice timing correction in SPM99 and SOA specification
5i) How do you enter empirically derived subject-specific HRF in SPM?
http://www-psych.stanford.edu/~kalina/SPM99/Tools/eHRF.html
Kalina Christoff
Aguirre,
G. K., Zarahn, E., & D'Esposito, M. (1998). The variability of
human, BOLD hemodynamic responses. Neuroimage, 8(4),
360-369.
D'Esposito, M., Zarahn, E., Aguirre, G. K., &
Rypma, B. (1999). The effect of normal aging on the coupling of
neural activity to the bold hemodynamic response. Neuroimage, 10(1),
6-14.
5j) How do you define user-specific HRF basis functions in SPM model specification?b
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=spm&O=D&F=&S=&P=44220
Date: Mon, 28 Apr 2008 11:35:47 -0700 From: Michael T Rubens Subject: Re: how to replace the hrf convolved reference function with a user specified one in spm?
5k) How do you estimate the parameters of the hemodynamic response function?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1003&L=spm&F=&S=&P=741845
Subject: Re: hemodynamic parameter estimation From: Karl Friston Date: Wed, 24 Mar 2010 17:25:21 +0000
5l) How do you enter a large number of subjects at once and then build a flexible factorial design?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=spm&F=&S=&P=607157
Subject: Re: flex factorial From: MCLAREN, Donald Date: Fri, 22 May 2009 15:43:00 -0500
5m) Temporal autocorrelation modelling for Multi-Band sequences:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1710&L=spm&F=&S=&P=717346
Subject: Re: DCM with multi-band fMRI data From:"Zeidman, Peter" Date: Mon, 30 Oct 2017 09:54:13 +0000
6a) How do you choose a high pass filter for event-related studies?
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0104&L=spm&P=R27646&I=3
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind9903&L=spm&P=R645&I=3
6b) How do you choose a high pass filter in SPM2?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0501&L=spm&O=D&F=&S=&P=18127
6c) How do you determine the high pass filter for your scanner/data?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=SPM&D=1&T=0&O=D&P=2567737
Date: Tue, 5 Dec 2006 10:41:16 +0100
From: PESENTI Mauro
Subject: Re: High-pass filter
6d) How do you check wether your design is fast enough to escape the high pass filter?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=SPM&T=0&O=D&P=135989
Date: Sun, 13 Apr 2008 21:00:14 +0200 From: Torben Ellegaard Lund Subject: high-pass filtering and spm_fMRI_design_show
6e) Code to decide on the best choice for the high pass filter:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901&L=SPM&T=0&O=D&P=116073
Subject: Re: high frequency cutoff depends on contrast? From: Jason Steffener Date: Fri, 16 Jan 2009 12:03:18 -0500
7a) Tutorial on Mathematics for Brain Imaging:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=spm&O=D&F=&S=&P=15932
Date: Tue, 8 Apr 2008 17:53:50 +0100 From: Will Penny Subject: Maths for Brain Imaging: Lecture Course Notes
7b) How do you calculate power estimates in SPM?
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind02&L=spm&P=R303408&I=3
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901&L=SPM&D=1&T=0&O=D&P=161900
Subject: Re: Question on VBM: How many subjects are enough to have statistical power? From: Roberto Viviani Date: Fri, 23 Jan 2009 10:20:55 +0100
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901&L=SPM&D=1&T=0&O=D&P=160455
Subject: Re: Question on VBM: How many subjects are enough to have statistical power? From: Christian Gaser Date: Fri, 23 Jan 2009 07:36:41 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0912&L=SPM&D=1&T=0&O=D&P=194579
Subject: Re: Power calculation From: Cyril Pernet Date: Wed, 23 Dec 2009 09:51:40 +0000
7c) Post-hoc “power” maps can be calculated for lesion maps in NPM (MriCron):
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=mricro&T=0&F=&S=&P=404
Date: Wed, 7 May 2008 15:09:40 +0100 From: Chris Rorden Subject: Re: power maps
7d) How do you obtain correlation coefficients?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&D=0&P=776465
Subject:Re: correlation coefficient in SPM2 From:Christian Gaser Date:Wed, 9 Feb 2005 08:42:52 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&D=0&P=5878188
Subject:Re: calculating correlation coefficient From:Christian Gaser Date:Mon, 14 Nov 2005 09:57:26 +0000
7e) How do you calculate correlations between regressors in data matrices?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0510&L=spm&O=D&F=&S=&P=36606
before acquiring datas: http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0510&L=spm&O=D&F=&S=&P=38345
(files stored in /usr/local/spm/add_ons/CalculateCorrelationsBeforefMRI)
7f) How do you correct for smoothness within a ROI?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0502&L=spm&O=D&F=&S=&P=39971
7g) How do you calculate partial correlations in SPM?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0507&L=spm&O=D&F=&S=&P=27755
7h) What is the difference between a covariate and a nuisance variable?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0507&L=spm&O=D&F=&S=&P=36320
7i) How do you convert T values in Z scores?
z_score = spm_t2z(t_score, degrees_of_freedom) t_score: comes from your SPM map degrees_of_freedom: at the bottom right of the SPM map
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind04&L=SPM&P=R376942&I=3&m=15543
(1) 1-cdf('t',Tstat,df)
or
(2) 1-spm_Tcdf(Tstat,df)https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1204&L=spm&F=&S=&P=228429
Subject:Re: get corresponding p value from T threshold From:"MCLAREN, Donald" Date:Wed, 11 Apr 2012 10:46:33 -0400
7j) Why in a model with hrf with time and dispersion derivatives is the T-test more powerful than the F-test?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0510&L=spm&O=D&F=&S=&P=12679
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0510&L=spm&O=D&F=&S=&P=14463
7k) How do you compute and interpret interactions in a 2x2 factorial design?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0511&L=spm&O=D&F=&S=&P=18159
(http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0511&L=spm&O=D&F=&S=&P=16695)
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1205&L=spm&F=&S=&P=253583
Subject:Re: Interpretation of 2x2 interaction effect From:"MCLAREN, Donald" Date:Wed, 9 May 2012 15:36:50 -0400
7l) How do you detect outlier subjects?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0512&L=spm&O=D&F=&S=&P=17198
http://www.sph.umich.edu/ni-stat/SPMd
7m) How do you report FDR corrected significance thresholds?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0601&L=spm&O=D&P=27832
7n) What are the disadvantages of using a FDR correction?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=spm&F=&S=&P=93399
Date: Wed, 10 Oct 2007 15:23:45 +0200 From: Roberto Viviani Subject: Re: FDR correction
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=spm&F=&S=&P=97598
Date: Wed, 10 Oct 2007 14:32:07 +0100 From: Laura Mancini Subject: Re: FDR correction
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=spm&F=&S=&P=115062
Date: Wed, 10 Oct 2007 16:41:56 -0500 From: Doug Burman Subject: Re: FDR correction
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=spm&F=&S=&P=123935
Date: Thu, 11 Oct 2007 15:11:01 +0200 From: Roberto Viviani Subject: Re: FDR correction
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=spm&F=&S=&P=78768
Date: Tue, 6 Nov 2007 18:34:03 -0500 From: Satoru Hayasaka Subject: Re: Q: Does FDR require "conceptual homogeneity" assumption?
7o) How do you solve an “Index exceeds matrix dimensions error in ReML estimation” in SPM2?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0602&L=spm&O=D&P=402
7p) How do you choose between the different ANOVA basic models in SPM2?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0605&L=spm&O=D&P=35596
Date: Thu, 25 May 2006 21:36:22 +0100 From: Rik Henson Subject: Re: ANOVA design matrix
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0605&L=spm&O=D&P=35704
Date: Thu, 25 May 2006 21:48:36 +0100 From: Rik Henson Subject: Re: ANOVA design matrix
7q) A didactic tutorial on the choice of different second-level statistical models:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0803&L=spm&F=&S=&P=189877
Date: Tue, 18 Mar 2008 09:44:35 +0000 From: Thomas Nichols Subject: Re: Multiple regression: testing an interaction at the second level
7r) How do you control for nonsphericity/covariance homogeneity (quality of the covariance estimate)?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0606&L=spm&O=D&P=27641
Date: Mon, 26 Jun 2006 15:15:54 -0400 From: Thomas E Nichols Subject: Re: Multi-Subject Realignment and Non-sphericity implementation questions
7s) How do you answer to the “replications are over?” question in random effect models?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0608&L=spm&O=D&P=40746
Date: Thu, 24 Aug 2006 02:51:35 -0700 From: Jan Gläscher Subject: Re: replications are over....
7t) How do you calculate percent signal change?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&O=D&F=&S=&P=310094
Date: Tue, 29 Aug 2006 02:37:03 -0700 From: Jan Gläscher Subject: Re: percent signal change
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0802&L=spm&O=D&F=&S=&P=30296
Date: Thu, 21 Feb 2008 18:25:16 -0800
Subject: Re: Concepts about percent signal change
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0802&L=spm&O=D&F=&S=&P=31057
Date: Fri, 22 Feb 2008 18:56:57 +0000 From: Paul Mazaika Subject: Re: Concepts about percent signal change
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0802&L=spm&O=D&F=&S=&P=31805
Date: Sat, 23 Feb 2008 12:15:30 -0500 From: Jeffrey P Lorberbaum Subject: Re: Concepts about percent signal change
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1005&L=SPM&D=1&O=D&P=163233
Subject: Re: Comparing % signal change From: cyril pernet Date: Thu, 20 May 2010 14:50:45 +0100
7u) How do you calculate percent signal change using the Anatomy Toolbox?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0608&L=spm&O=D&P=49688
Date: Thu, 31 Aug 2006 11:36:11 +0200 From: "Simon B. Eickhoff" Subject: Re: Anatomy toolbox clarifications http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0609&L=spm&O=D&P=9082 Date: Thu, 7 Sep 2006 10:11:13 +0200 From: "Simon B. Eickhoff" Subject: Re: extract values from SPM Anatomy toolbox
7v) How do you assess the signal homogeneity across voxels in a ROI?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0609&L=spm&O=D&P=43904
Date: Thu, 28 Sep 2006 10:55:16 +0100 From: cyril pernet Subject: Re: FRISTON et al. vs. SAXE et al. 2006
7w) When is it necessary to correct for nonsphericity and for correlated measures in 2nd level statistic models?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0609&L=spm&O=D&P=46739
Date: Fri, 29 Sep 2006 10:47:54 +0100 From: Alexa Morcom Subject: Re: IDD data and POOLED errors
7x) How do you choose “independence” and “unequal variance” options in factorial designs in SPM5?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=spm&F=&S=&P=354253
Date: Mon, 15 Jan 2007 09:20:07 +0100 From: Volkmar Glauche Subject: Re: Conditions in FLEXIBLE factorial
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=spm&F=&S=&P=382702
Date: Mon, 15 Jan 2007 22:51:55 +0100 From: Volkmar Glauche Subject: Re: I: [SPM] Conditions in FLEXIBLE factorial
7y) How do you model subject x time interactions (e.g. FDG-PET)?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0802&L=spm&O=D&F=&S=&P=34688
Date: Wed, 27 Feb 2008 15:39:46 +0000 From: Thomas Nichols Subject: Re: Subject x Time interaction contrast definition question (SPM5)
7z) Choice of statistical thresholds:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0803&L=spm&F=&S=&P=42069
Date: Thu, 6 Mar 2008 00:25:30 +0000 From: Thomas Nichols Subject: Re: vbm: FDR/ p<0.01
7a1) Tutorial on contrast weights:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0803&L=spm&O=D&F=&S=&P=16237
Date: Mon, 17 Mar 2008 23:27:34 -0700 From: Jan Gläscher Subject: tutorial on contrast weights
7b1) How do you convert a T-map into a r-map?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=spm&O=D&F=&S=&P=11349
Date: Mon, 7 Apr 2008 07:21:41 +0100 From: Christian Gaser Subject: Re: Transforming T-maps
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=spm&O=D&F=&S=&P=11569
Date: Mon, 7 Apr 2008 07:32:35 +0100 From: Christian Gaser Subject: Re: Transforming T-maps
7c1) How do you setup a contrast for quadratic polynomial learning effects across blocks?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=spm&O=D&F=&S=&P=46669
Date: Tue, 29 Apr 2008 15:04:51 -0700 From: Jan Gläscher Subject: Re: Questions about getting learning effect ... and regarding parametric modulation regressors:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=spm&O=D&F=&S=&P=46932
Date: Tue, 29 Apr 2008 18:11:54 -0700 From: Jan Gläscher Subject: Re: Questions about getting learning effect
7d1) How do you use contrast masking to discriminate activations from deactivations?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=spm&F=&S=&P=261879
Date: Fri, 16 May 2008 11:17:41 +0200 From: "[log in to unmask]" Subject: deactivation in 2-nd level analysis
7e1) How do you detect potential artifacts related to low smoothness (high RPV)?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=spm&O=D&F=&S=&P=27565
Date: Tue, 20 May 2008 21:47:00 +0100 From: Thomas Nichols Subject: Re: Resel calculation problem in VBM
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=spm&O=D&F=&S=&P=27683
Date: Tue, 20 May 2008 23:49:50 +0200 From: Volkmar Glauche Subject: Re: Resel calculation problem in VBM
7f1) How do you calculate voxel to resel correspondence?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=spm&O=D&F=&S=&P=39761
Date: Fri, 30 May 2008 04:06:19 +0100 From: Anderson Winkler Subject: Re: Relatioin between voxels and resels
7g1) How do you specify mixed HRF and FIR models?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0806&L=spm&O=D&F=&S=&P=9300
Date: Wed, 4 Jun 2008 11:40:01 -0700 From: Jan Gläscher Subject: Re: FIR models and variable block length
7h1) How do you set the minimal distance between voxels and the maximum number of reported cluster maxima in SPM tables?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0809&L=spm&F=&S=&P=75209
Subject: Re: distance between peaks in results table From: Darren Gitelman Date: Thu, 4 Sep 2008 21:53:40 -0500
7i1) How do you extract individual clusters as a binary image from an activation map?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0811&L=SPM&O=D&P=146391
Subject: Re: saving individual clusters as binary images From: Guillaume Flandin Date: Tue, 18 Nov 2008 19:28:15 +0000
7j1) What do 'fitted' (variable Y) and 'adjusted' (variable y) responses correspond to in the plot results routine?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901&L=spm&F=&S=&P=488819
Subject: Re: SPM5 - Plot Fiited responses From: Cyril Pernet Date: Wed, 21 Jan 2009 10:34:27 +0000
7k1) How do you activate topological FDR as described in Chumbley & Friston (2008) in SPM8b?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=SPM&T=0&O=D&P=135031
Subject: Re: FDR combined with cluster extent From: Guillaume Flandin Date: Thu, 19 Mar 2009 11:15:16 +0000
7l1) What is the recommended procedure to apply topological FDR in SPM8?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=spm&F=&S=&P=341930
Subject: Re: topological FDR in SPM8 From: Guillaume Flandin Date: Mon, 6 Apr 2009 19:22:05 +0100
7m1) Do you have to correct for uneven group size in specifying two-sample t-test contrasts?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=spm&F=&S=&P=509554
Subject: Re: Uneven group size t-test contrasts From: "Stephen J. Fromm" Date: Fri, 10 Apr 2009 11:43:51 +0100
7n1) How do you output result tables restricted to a specific VOI in SPM?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0906&L=spm&F=&S=&P=289336
Subject: Re: Results script modification to get SVC From: Chris Watson Date: Thu, 11 Jun 2009 15:59:20 -0400
7n1b) How do you save an image of significant voxels within a SVC volume?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;3e6ede29.1006
Subject:Re: extracting cluster after small volume correction (SVC) From:Guillaume Flandin Date:Thu, 24 Jun 2010 13:19:20 +0100
Created file spm_VOI.m.saveSVCimg
cp -a /usr/local/spm/spm12/spm_VOI.m.saveSVCimg /usr/local/spm/spm12/spm_VOI.m
Run SVC as usual, this will create a SVC.nii image in your stats folder.
when finished:
cp -a /usr/local/spm/spm12/spm_VOI.m.orig /usr/local/spm/spm12/spm_VOI.m
7o1) Full vs flexible factorial design for within-subject factorial designs (no between group factor):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0909&L=spm&F=&S=&P=492053
Subject: Re: Full vs Flexible Factorial From: lion gao Date: Thu, 24 Sep 2009 01:44:26 +0800
7p1) Multivariate factorial analysis vs. one-sample t-tests (also regards SPM flexible factorial vs GLMFlex error partitioning):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0910&L=spm&F=&S=&P=400168
Subject: Re: Multifactorial designs at the second level From: Rik Henson Date: Fri, 16 Oct 2009 16:55:35 +0100
(also see the related “flexible factorial - main effect of subject factor“ thread, e.g.,
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=spm&F=&S=&P=353475
Subject: Re: flexible factorial - main effect of subject factor From: "MCLAREN, Donald” Date: Mon, 6 Apr 2009 15:28:00 -0500
and the proposed solution for the flexible factorial error partitioning problems, using two-sample t-tests instead:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1001&L=spm&F=&S=&P=648392
Subject: Re: 2x2x2 repeated measures ANOVA partitioned errors - second level analyis From: "MCLAREN, Donald" Date: Wed, 27 Jan 2010 08:47:44 -0600)
further clarification:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=spm&F=&S=&P=649935
Subject: Re: flexible facorial in spm5 From: "MCLAREN, Donald" Date: Sun, 14 Feb 2010 14:14:18 -0600
other clarifications:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1101&L=spm&F=&S=&P=883572
Subject:Re: Design matrix for each or all subject(s)? From:Rik Henson Date:Fri, 28 Jan 2011 12:38:30 +0000
further useful clarification:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;d29f4403.1106
Subject: Re: flexible factorial designs and contrasts From: "MCLAREN, Donald" Date: Tue, 21 Jun 2011 14:47:35 -0400
still other clarifications:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1109&L=SPM&F=&S=&P=65554
Subject:Re: Question regarding sphericity and design From:"MCLAREN, Donald" Date: Fri, 2 Sep 2011 10:30:35 -0400
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1109&L=SPM&F=&S=&P=86440
Subject: Re: Question regarding sphericity and design From: "MCLAREN, Donald" Date: Fri, 2 Sep 2011 16:10:34 -0400
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1109&L=SPM&F=&S=&P=131054
Subject: Flexible Factorial Models From: "MCLAREN, Donald" Date: Tue, 6 Sep 2011 18:52:57 -0400
conclusive (?):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1201&L=spm&D=1&T=0&O=D&P=422029
Subject:Re: Repeated measures ANOVA vs. SPM full factorial From:"MCLAREN, Donald" Date:Mon, 23 Jan 2012 11:45:58 -0500
other examples/explanations:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&D=0&P=717318
Subject:Re: Deciding which effects to include in a flexible factorial model From:"MCLAREN, Donald" Date:Wed, 29 Feb 2012 16:51:33 -0500
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&D=0&P=722826
Subject:Re: Deciding which effects to include in a flexible factorial model From:"MCLAREN, Donald" Date:Wed, 29 Feb 2012 17:26:26 -0500
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1204&L=spm&F=&S=&P=46
Subject:Re: 2x2 within-subjects ANOVA: Flexible Factorial and hierarchical approach produce different results From:"MCLAREN, Donald" Date:Sun, 1 Apr 2012 02:15:30 -0400
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1311&L=spm&F=&S=&P=293319
Subject:Re: Flexible factorial - is it valid? From:Rik Henson Date:Thu, 14 Nov 2013 16:41:05 +0000
...the definitive one!:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;b5fb4fb.1503
Subject:Re: Flexible factorial ANOVA advice From:"MCLAREN, Donald" Date:Tue, 17 Mar 2015 11:25:17 -0400
More and more... very useful ones, actually:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1504&L=spm&F=&S=&P=857449 Subject:Re: Flexible factorial inclusion of subject effect From:"H. Nebl" Date:Thu, 30 Apr 2015 16:34:30 +0100 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1504&L=spm&F=&S=&P=866794 Subject:Re: Flexible factorial inclusion of subject effect From:"H. Nebl" Date:Thu, 30 Apr 2015 17:38:29 +0100
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1504&L=spm&F=&S=&P=877724
Subject:Re: Flexible factorial inclusion of subject effect From:Guillaume Flandin Date:Thu, 30 Apr 2015 19:11:54 +0100
7q1) How do you calculate F degrees of freedom?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0911&L=SPM&T=0&O=D&P=36397
Subject: Re: Factorial Design w/ Partitioned Error, are DFs incorrect? From: Rik Henson Date: Wed, 4 Nov 2009 09:35:55 +0000
7r1) How do export SPM statistic tables to Excel files?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=spm&F=&S=&P=816052
Subject: Re: Is there a way to save the table of statistics result? From: Guillaume Flandin Date: Thu, 25 Feb 2010 16:59:20 +0000
But even better: !!!
diary(['MyTable.txt'])
spm_list('TxtList', TabDat, 1);
diary off
7s1) Methods for checking goodness of data fitting across models:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1005&L=SPM&D=1&O=D&P=39181
Subject: Re: full factorial - is my model correct? From: DRC SPM Date: Thu, 6 May 2010 11:25:39 +0100
7t1) Null/Global/Intermediate conjunction and independence of data spaces:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1005&L=spm&F=&S=&P=100202
Subject: Re: full factorial - is my model correct? From: DRC SPM Date: Thu, 6 May 2010 11:25:39 +0100
7u1) How do you report 'Inf' (i.e. infinity) Z scores indicated in SPM coordinate tables?
>8
Subject: Re: inf values for z-scores at the voxel level From: "Hammers, Alexander" Date:Sun, 28 Oct 2007 15:40:46 -0000
7v1) How do you set the initial threshold for cluster extent inference and what does a positive result mean?
Subject:Re: Thresholds for visualization of clusters vs. voxels From:Donna Dierker Date:Thu, 24 Jun 2010 14:49:51 -0500
7w1) How do you model the Variance across Conditions/Groups in the comparison single patient vs group in SPM8?
→ Equal!
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1101&L=spm&F=&S=&P=454798
Subject: Re: single subject analysis with SPM8 From: Rik Henson Date: Wed, 19 Jan 2011 12:01:39 +0000 see also : http://www.mrc-cbu.cam.ac.uk/people/rik.henson/personal/ /usr/local/spm/Henson_Singlecase_06.pdf
7x1) When do you better use explicit masking vs Small Volume Correction?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;140baa5f.1101
Subject:Re: SVC vs. Explicit Mask From:Dr Cyril Pernet Date:Mon, 31 Jan 2011 10:10:46 +0000
7x1b) Need to correct form multiple tests with Small Volume Correction:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1401&L=spm&F=&S=&P=150364
Subject:Re: Small Volume Correction, and Video Tutorial wanted From:"MCLAREN, Donald" Date: Thu, 9 Jan 2014 09:49:35 -0500
7y1) Is it better to include or not to include the Subject Factor in Within-subject ANOVA designs?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1109&L=SPM&F=&S=&P=241747
Subject:Re: full vs flexible factorial design within subjects From:"Penny, William" Date:Mon, 12 Sep 2011 10:30:03 +0000
7z1) What is the recommended lower limit on a cluster-forming threshold to ensure accurate inferences?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1105&L=fsl&F=&S=&P=89386
Subject:Re: poststats inquiry pls From: Thomas Nichols Date:Tue, 10 May 2011 10:06:50 +0100
7z1.b) How do you calculate the corrected cluster size threshold for given cluster-defining threshold?
http://www-personal.umich.edu/~nichols/JohnsGems5.html#Gem6
>> CorrClusTh.m
7z1.c) Afni 3dclustsim % alphasim method for calculating cluster size threshold:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1312&L=spm&F=&S=&P=265175
Subject: Re: 3dClustsim question From: Mark Date:Tue, 10 Dec 2013 06:56:34 +0000
7a2) Thread on the use of the GLMFlex Toolbox (http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/GLM_Flex.html):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&D=0&P=622719
Subject:Re: 2x3x3 ANOVA (within-subject) From:"MCLAREN, Donald" Date: Sat, 25 Feb 2012 13:06:04 -0500
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&D=0&P=624929
Subject:Re: 2x3x3 ANOVA (within-subject) From:"MCLAREN, Donald" Date:Sat, 25 Feb 2012 16:03:30 -0500
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&D=0&P=636632
Subject:Re: 2x3x3 ANOVA (within-subject) From:"MCLAREN, Donald" Date:Sun, 26 Feb 2012 19:28:46 -0500
7b2) Brain mask and variable degrees of freedom:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1203&L=spm&F=&S=&P=525738
Subject: Re: Missing voxels From:"MCLAREN, Donald" Date:Sat, 17 Mar 2012 13:44:18 -0400
7c2) Ways to combine hrf + derivatives in a single contrast:
Calhoun, V. D., Stevens, M. C., Pearlson, G. D., & Kiehl, K. A. (2004). fMRI analysis with the general linear model: removal of latency-induced amplitude bias by incorporation of hemodynamic derivative terms. Neuroimage, 22(1), 252–257. doi:10.1016/j.neuroimage.2003.12.029
Steffener, J., Tabert, M., Reuben, A., & Stern, Y. (2010). Investigating hemodynamic response variability at the group level using basis functions. Neuroimage, 49(3), 2113–2122. doi:10.1016/j.neuroimage.2009.11.014
http://sites.google.com/site/steffener/Papers
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;7fba87b3.0811
Subject:Contrast of conditions including temporal and dispersion derivatives From:Christopher Benjamin Date:Wed, 5 Nov 2008 15:49:43 +0000
Subject:Re: HRF + derivatives From:Jason Steffener Date:Wed, 14 Mar 2012 09:54:51 -0400
7d2) How do you perform a conjunction analyses between 3 distinct experiments?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1207&L=spm&F=&S=&P=96758
Subject:Re: Group conjuction analysis across three experiments From:"MCLAREN, Donald" Date:Mon, 9 Jul 2012 13:07:50 -0400
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1207&L=spm&F=&S=&P=103748
Subject:Re: Group conjuction analysis across three experiments From:"MCLAREN, Donald" Date:Mon, 9 Jul 2012 22:41:13 -0400
7e2) Update on testing 2nd-level design contrasts for factors and covariates:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1510&L=spm&F=&S=&P=826644
(see thread)
Subject:Re: Use of multiple contrasts in a second level factorial design From:"Penny, William" Date:Fri, 30 Oct 2015 14:34:50 +0000
7f2) Correct procedure for Small Volume Correction:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1602&L=spm&F=&S=&P=445540
Subject: Re: Is a 10 mm volume very large for small volume correction? From: "MCLAREN, Donald" Date: Fri, 19 Feb 2016 11:34:31 -0500
7f2) More on correct procedures for Small Volume Correction:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1609&L=spm&D=0&P=51926
Subject:Re: initial threshold for small volume correction From:MRI More Date:Sun, 4 Sep 2016 19:38:02 +0100
particularly:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1609&L=spm&D=0&P=6310
Subject:Re: initial threshold for small volume correction From:MRI More Date:Thu, 1 Sep 2016 14:41:00 +0100
7g2) On basics of planned and post-hoc multiple comparisons:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;4d46c459.1701
Subject:Re: Post-Hoc ANOVA Inquiry From: MRI More Date:Thu, 12 Jan 2017 19:03:04 +0000
8. Statistics for event-related designs
8a) How do I model self-paced event-related designs?
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0207&L=spm&P=R23987&I=3
http://abstracts.academicpress.com/ViewAbstract.asp?AbstractID=15530
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0208&L=spm&P=R1155&I=3
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0403&L=spm&P=R2&I=3
8b) How do I model resposes with duration > ~ 1 s?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0510&L=spm&O=D&F=&S=&P=36489
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0510&L=spm&O=D&F=&S=&P=36606
8c) How do I model reaction times (RT) in an event-related design?
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=spm;58e72a0.04
Subject:Re: RT as covariate From: Rik Henson Date:Fri, 28 May 2004 13:38:31 +0100
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=spm&F=&S=&P=24974
Subject: Re: How do regressors compete for variance if not orthogonalized?
From: cyril pernet
Date: Wed, 4 Mar 2009 11:38:44 +0000https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=spm&F=&S=&P=44681
Subject: Re: How do regressors compete for variance if not orthogonalized? From: cyril pernet Date: Wed, 4 Mar 2009 15:10:44 +0000 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=spm&F=&S=&P=46856 Subject: Re: How do regressors compete for variance if not orthogonalized? From: "Dorian P." Date: Wed, 4 Mar 2009 16:56:42 +0100
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1610&L=spm&F=&S=&P=524359
Subject:Re: the calculation of the latency of the BOLD response and the explaination of the temporal derivative of parametric regressor From:Colin Hawco Date:Fri, 14 Oct 2016 11:51:36 -0400 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1610&L=spm&F=&S=&P=538888 Subject:Re: the calculation of the latency of the BOLD response and the explaination of the temporal derivative of parametric regressor From:PERNET Cyril Date:Sat, 15 Oct 2016 13:03:08 +0000
8c) How do you turn off orthogonalization of parametric regressors by spm_orth.m?
http://imaging.mrc-cbu.cam.ac.uk/imaging/ParametricModulations
Important! In case orthogonalization is turned off, you need to manually demean the parametric modulators/regressors!
https://groups.google.com/forum/#!msg/wagerlabtools/Au9-xCDxLRk/ory1ahwMhqEJ
8d) How do you set up contrasts for a Finite Impulse Response (FIR) model?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind01&L=spm&O=D&F=&S=&P=214392
Date: Thu, 13 Sep 2001 16:10:23 +0100 From: Rik Henson Subject: Re: FIR basis and second level analyses
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&O=D&F=&S=&P=39773
Date: Tue, 1 Feb 2005 21:58:28 -0000 From: Rik Henson Subject: Re: trouble specifying first level From: Marko Wilke Date:Mon, 8 Dec 2008 16:46:48 +0100 Subject: Re: time course of activation
8f) How do you calculate Global and Null conjunction analyses in ImCalc?
Subject:Re: SnPM and conjunction analysis From:"Thomas E. Nichols" Date:Mon, 29 Nov 2004 16:40:12 -0500
Subject:Re: Conjunction analysis with 2nd-level-t-test From:"Dominik R. Bach" Date:Mon, 11 Dec 2006 17:53:37 +0100
8g) Which images do you enter in a second-level analysis?
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind04&L=spm&P=R342964&I=3
8h) How do you handle subject with 100% accuracy rate in a correct/error response model?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0812&L=spm&D=1&T=0&O=D&P=11279
Subject: Re: trouble specifying first level From: Marko Wilke Date:Mon, 8 Dec 2008 16:46:48 +0100
8i) How do you design and analyze event-related studies with sparse sampling?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0810&L=SPM&P=R65325&m=31694
Subject: Re: DCM of sparse temporal sampling
From: Stefan Kiebel
Date:Tue, 28 Oct 2008 09:09:07 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=SPM&P=R24290&m=31694
Subject: Re: Sparse Temporal Sampling analysis
From: Simon Durrant
Date: Mon, 12 May 2008 08:47:12 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=SPM&P=R19474&m=23597
Subject: Re: FIR analysis and sparse sampling design
From: Catherine Wan
Date: Mon, 7 Apr 2008 13:25:08 +1000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0802&L=SPM&P=R25652&m=23597
Subject: Re: Sparse efMRI, TR, Interscan Interval & SOTs
From: Greig de Zubicaray
Date: Fri, 15 Feb 2008 13:09:47 +1000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=SPM&P=R128481&m=17843
Subject: Re: sparse temporal sampling data analysis
From: Satrajit Ghosh
Date: Sat, 19 Mar 2005 01:50:06 -0500
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=SPM&P=R64238&m=17843
Subject: Re: Settings for Sparse sampling in SPM2
From: Matt Davis
Date: Thu, 3 Feb 2005 18:12:39 +0000
8j) How do you model compound events for which the exact onset is unknown (e.g. sentences)?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=SPM&D=1&T=0&O=D&P=45924
Subject: Re: modeling compound events
From: Kasper Winther Jørgensen
Date: Fri, 3 Apr 2009 17:20:45 -0700
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=SPM&D=1&T=0&O=D&P=46595
Subject: Re: modeling compound events
From: Eric Zarahn
Date: Fri, 3 Apr 2009 22:25:04 -0400
See also: /media/hda5/Data/Bibliografia/Technicals/HutchinsonRA_Neuroimage2009.pdf
8k) How do you specifically analyze the latency of hrf responses at the second-level?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0911&L=SPM&D=1&T=0&O=D&P=266567
Subject: Re: Latency (temp deriv) in 2nd level (Henson) From: Rik Henson Date: Fri, 27 Nov 2009 12:17:07 +0000
8l) Problems with Finite Impulse Response and matrix orthogonalization for estimation of the shape of the hemodynamic response:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1109&L=SPM&D=0&P=53151
Subject:Unexpected response when using a FIR analysis From:"Klooster, Debby" Date:Fri, 2 Sep 2011 09:55:08 +0200
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1109&L=SPM&D=0&P=187016
Subject: Re: Unexpected response when using a FIR analysis From:Hannes Ruge Date:Thu, 8 Sep 2011 08:23:37 +0100
8m) Ways to account for different number of trials across conditions:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1610&L=spm&F=&S=&P=553604
Subject:Re: concatenate sessions/runs From:"MCLAREN, Donald" Date:Sun, 16 Oct 2016 20:45:26 -0400
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0806&L=spm&F=&S=&P=9069
Subject:Re: Unequal number of trials per condition in event-related design From:Cyril Pernet Date:Sun, 1 Jun 2008 09:10:23 +0100
9. Statistical Nonparametric Mapping (SnPM)
9a) How do you assess non-parametric conjunctions analyses?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0411&L=spm&O=D&F=&S=&P=29398
9b) What is the purpose of "Aprrox. tests"?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0501&L=spm&O=D&F=&S=&P=25647
9c) Snpm8b and advantages of permutation analysis:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;8d10c0d6.1007
Subject: Re: SnPM From: Thomas Nichols Date: Wed, 7 Jul 2010 10:39:21 +0100
10. Psycho-Physiological Interactions
10a) How do you perform a PPI in SPM5?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709&L=spm&O=D&F=&S=&P=30211
Date: Thu, 27 Sep 2007 16:27:43 -0500 From: Darren G Subject: Re: Trying PPI for the first time
10b) How is directionality of PPI encoded in SPM?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=SPM&D=1&T=0&O=D&P=51618
Subject: Re: Question regarding PPI interpretation From: Karl Friston Date: Tue, 10 Mar 2009 18:18:04 +0000
10c) On the (lack of) circularity of data in PPI (and DCM) analyses:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1012&L=SPM&D=0&P=37067
Subject: Is there the circularity of data in PPI? From:Karl Friston Date:Thu, 2 Dec 2010 14:16:46 +0000
10d) Remarks on contrast orthogonality for physiological and psychological regressors definition:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1103&L=SPM&F=&S=&P=253787
Subject:Re: A quick question concerning the PPI analysis From:Karl Friston Date:Wed, 23 Mar 2011 15:36:34 +0000
10e) Functional connectivity toolbox
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1106&L=spm&F=&S=&P=190620
Subject:Re: Functional Connectivity From:Raphael Hilgenstock Date:Mon, 13 Jun 2011 17:05:13 +0200
10f) How do you interpret a negative PPI interaction?
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind05&L=SPM&P=R276113&1=SPM&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
Subject:Re: PPI interpretation From:"Dr P.C. Fletcher" Date:Thu, 9 Jun 2005 16:11:01 +0100
10g) How do you plot a PPI group effect?
Subject:Re: Plotting a PPI Effect From:"MCLAREN, Donald" Date:Tue, 6 Sep 2011 16:39:03 -0400
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1304&L=spm&D=0&P=265382
Subject: Re: PPI plotting groups From: "MCLAREN, Donald" Date:Tue, 9 Apr 2013 16:20:44 -0400
10h) Tips on editing the gPPI ppi_wrapper:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1207&L=spm&F=&S=&P=247701
Subject:Re: gPPI - editing the ppi_wrapper and input structure From:Sophie Forster Date:Wed, 18 Jul 2012 20:11:57 +0100
1aaa) Robustness and general DCM approach
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;ec3f1e9e.1711
Subject: Re: Robustness of DCM parameter estimation From: "Zeidman, Peter" Date: Tue, 21 Nov 2017 10:57:47 +0000
11aa) General advices on setting up a DCM model
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0907&L=spm&F=&S=&P=247671
Subject: Re: DCM Design From: Klaas Enno Stephan Date: Fri, 10 Jul 2009 08:44:58 +0000
11a) How do you differentially model the modulatory effects of two conditions A and B?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=2021390
Date: Tue, 2 May 2006 10:47:54 +0100 From: Klaas Enno Stephan Subject: Re: Another DCM question
11b) How do you interpret a negative or positive value of the A and B matrix?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=2025837
Date: Tue, 2 May 2006 10:49:00 +0100 From: Klaas Enno Stephan <[logintounmask]> Subject: Re: questions on interpreting significant DCM data?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0711&L=spm&F=&S=&P=250526
Date: Mon, 19 Nov 2007 21:12:21 -0600 From: d gitelman Subject: Re: negative rates in DCM
update...
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1008&L=spm&F=&S=&P=3867
Subject:Re: How to interpret negative values in DCM? From: Klaas Enno Stephan Date: Sun, 1 Aug 2010 21:18:47 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1304&L=spm&F=&S=&P=350426
Subject:Re: DCM model intrinsic and modulatory connections From:"Friston, Karl" Date:Thu, 11 Apr 2013 17:08:11 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;df32c9c1.1405
Subject:Re: Network Discovery with DCM From:"Zeidman, Peter" Date: Fri, 16 May 2014 15:01:35 +0000
11c) How do you interpret a negative value in the C matrix?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=2027941
Date: Tue, 2 May 2006 10:50:08 +0100 From: Klaas Enno Stephan <[logintounmask]> Subject: Re: dcm - more questions...
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=4495568
Date: Mon, 18 Sep 2006 17:59:18 +0100 From: Klaas Enno Stephan Subject: Re: spm_dcm_average query
11d) How do you use the compare tool in DCM?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=2213938
Date: Sat, 13 May 2006 18:27:46 +0100 From: Klaas Enno Stephan <[logintounmask]> Subject: Re: DCM model justification - question for DCM experts
11e) Can you model the effects of region A on the connection between regions B&C? -> not for the moment
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0609&L=spm&O=D&P=14605
Date: Mon, 11 Sep 2006 21:25:07 +0100 From: Klaas Enno Stephan Subject: Re: higher-order interactions in DCM
11f) SEM compared to DCM
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=4710743
Date: Wed, 27 Sep 2006 10:01:46 +0100 From: James Rowe Subject: Re: DCM questions
11g) How do you setup a 2x2 factorial design for DCM?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=spm&F=&S=&P=64368
Date: Wed, 2 Apr 2008 18:18:25 +0000 From: Klaas Enno Stephan Subject: AW: [SPM] DCM and 2x2 factorial design
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=SPM&P=R592539&I=-3
Date: Fri, 20 Oct 2006 21:30:13 +0100 From: Klaas Enno Stephan Subject: Re: DCM advice ...
11h) Should global scaling be used for DCM analyses?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=SPM&P=R62901&I=-3
Date: Mon, 23 Feb 2004 22:08:05 +0000 From: Klaas Enno Stephan Subject: Re: DCM and negative modulation - followup
11i) How do you set up a design matrix with multiple conditions and differential connectivity effects for DCM analysis?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=spm&F=&S=&P=175714
Date: Tue, 9 Jan 2007 19:22:08 +0000 From: Klaas Enno Stephan Subject: Re: FW: help with design matrix for DCM analysis
11j) Can I use SPM5 to specify and estimate a design model using a SPM.mat matrix created in SPM2?
Yes, and it is advisable to use SPM5 for DCM instead of SPM2!
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=spm&F=&S=&P=433299
Date: Thu, 18 Jan 2007 12:05:25 +0000 From: Klaas Enno Stephan Subject: Re: DCM result interpretation
11k) Which approach is preferable for extracting subject-specific VOIs?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=spm&F=&S=&P=436158
Date: Thu, 18 Jan 2007 11:33:11 +0000 From: Klaas Enno Stephan Subject: Re: VOI extraction for DCM
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1407&L=spm&D=0&P=752093
Subject:Re: DCM: Group comparison & defining ROIs From:"Zeidman, Peter" Date:Tue, 29 Jul 2014 15:52:23 +0000 see also: Zaghlool, S. & Wyatt, C. Front. Neurosci 8, 191 (2014).
11l) What do mean values in averaged DCM models represent?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=SPM&P=R553189&I=-3
Date: Wed, 8 Dec 2004 18:21:28 +0000 From: Will Penny Subject: Re: DCM - Average
11m) Are Bayes mean statistics in DCM-SPM5 sensitive to outliers?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=spm&F=&S=&P=413206
Date: Fri, 23 May 2008 18:09:07 +0000 From: Klaas Enno Stephan Subject: AW: Quick DCM question
11n) In which case is it better to concatenate sessions for DCM analyses?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0712&L=spm&F=&S=&P=394536
Date: Fri, 28 Dec 2007 09:12:00 -0600 From: d gitelman Subject: Re: DCM with multiple sessions per subject
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1301&L=spm&F=&S=&P=281230
Subject:Re: Repeated-measures, group DCM From: Penny, William" Date:Tue, 15 Jan 2013 12:24:10 +0000
11o) How do you include additional regressors modelling separate sessions for DCM concatenation?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0801&L=spm&F=&S=&P=203682
Date: Fri, 11 Jan 2008 00:27:18 -0600 From: d gitelman Subject: Re: regressors for concatenation If you had runs = 6 scans = 100 (number of scans per run): >>r = kron(eye(runs-1),ones(scans,1));
also disable AR(1) function:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=spm&F=&S=&P=543851
Subject: Re: combining 2 runs and specifying multiple conditions in the one file From: "MCLAREN, Donald" Date: Sun, 14 Feb 2010 23:07:18 -0600
also estimate the high-pass filter separately for each session in the concatenated design matrix:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;83843cc8.1502
Subject:Re: Design matrix for DCM with multiple sessions From:"Zeidman, Peter" Date:Mon, 2 Feb 2015 18:57:34 +0000
Important update:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1510&L=spm&F=&S=&P=10385
Subject:Re: dcm From:"Zeidman, Peter" Date: Thu, 1 Oct 2015 09:10:59 +0000
See: https://en.wikibooks.org/wiki/SPM/Concatenation
11p) What do the AIC and BIC parameters in the Bayesian model comparison refer to?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0801&L=spm&F=&S=&P=362859
Date: Sun, 20 Jan 2008 19:33:12 +0000 From: Klaas Enno Stephan Subject: Re: Questions about comparing DCMs using SPM5
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0801&L=spm&F=&S=&P=375292
Date: Mon, 21 Jan 2008 09:48:31 +0000 From: Klaas Enno Stephan Subject:
11q) How do you define slice timing within DCM?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0803&L=spm&F=&S=&P=269565
Date: Sat, 22 Mar 2008 15:04:35 +0000 From: Nia Goulden Subject: Re: Slice Timing Issue in DCM (SPM5)
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1010&L=spm&F=&S=&P=234456
Subject:Re: DCM: slice timing question From:Darren Gitelman Date:Mon, 11 Oct 2010 19:41:36 -0500
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&F=&S=&P=495050
Subject:Re: delays vector in DCM From:Hanneke den Ouden Date:Mon, 20 Feb 2012 18:41:09 -0500
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;f51cda1b.1510
Subject:Re: DCM.delays inquiry From:Rita Elena Loiotile Date:Mon, 5 Oct 2015 16:19:00 -0400
11r) How do you choose the threshold (Hz) for reviewing DCM models?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0804&L=spm&F=&S=&P=68534
Date: Wed, 2 Apr 2008 18:19:43 +0000 From: Klaas Enno Stephan Subject: AW: [Fwd: Re: DCM Analysis]
11s) How do you batch multiple DCM model estimations?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=spm&F=&S=&P=434334
Date: Tue, 27 May 2008 17:22:57 +0100 From: Mohamed Seghier Subject: Re: batching DCM estimations in SPM5
11t) How do you batch multiple DCM model specifications?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0806&L=spm&F=&S=&P=314458
Date: Wed, 18 Jun 2008 18:08:01 +0100 From: Guillaume Flandin Subject: Re: A question about Batch file For DCM
For SPM12b:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;ba21aa08.1408
Subject:Re: DCM model specification script From:"Zeidman, Peter" Date:Thu, 14 Aug 2014 09:59:40 +0000
11u) How do you obtain group-level values from DCM model comparison?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0806&L=spm&F=&S=&P=441059
Date: Wed, 25 Jun 2008 07:41:22 +0000 From: Klaas Enno Stephan Subject: AW: [SPM] Comparing Models in DCM across subjects!
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0811&L=spm&F=&S=&P=509265
Subject: AW: [SPM] Different ways for group model comparison with DCM? From: Klaas Enno Stephan Date: Fri, 28 Nov 2008 15:12:19 +0000
see also: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=spm&F=&S=&P=561926
Subject: DCM: fixed vs. random effects BMS; direction of connectivity change From: Narender Ramnani Date: Fri, 22 May 2009 09:23:54 +0100
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=spm&F=&S=&P=825353
Subject: Re: DCM: fixed vs. random effects BMS; direction of connectivity change From: Klaas Enno Stephan Date: Fri, 29 May 2009 09:32:53 +0000
11v) How to get some diagnostics to ensure model inversion has converged:
>> help spm_dcm_fmri_check
>> spm_dcm_fmri_check
Very useful mail regarding checking signal variance explained by VOIs and model fits:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1410&L=spm&F=&S=&P=407764
Subject:Re: DCM users From:"Zeidman, Peter" Date:Mon, 13 Oct 2014 16:40:20 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;2d0e6b1b.1404
Subject:Re: Low variance explained in DCM From:"Zeidman, Peter" Date:Fri, 25 Apr 2014 11:13:58 +0000 load VOI_xxx.mat; 100*xY.s(1)/sum(xY.s) https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;72129216.1508 Subject:Re: DCM Bayes Factor comparison From:"Zeidman, Peter" Date:Thu, 13 Aug 2015 08:19:02 +0000
Plot of parameter estimates:
figure,spm_plot_ci(DCM.Ep,DCM.Cp)
11w) Is it legitimate to perform a DCM analysis on areas that do not show a GLM effect?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0708&L=spm&F=&S=&P=521147
Subject: Re: DCM - VOIs and clinical groups From: Klaas Enno Stephan Date: Fri, 31 Aug 2007 17:22:04 +0100
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709&L=spm&F=&S=&P=45681
Subject: Re: DCM - VOIs and clinical groups From: Klaas Enno Stephan Date: Wed, 5 Sep 2007 14:39:04 +0100
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0810&L=spm&F=&S=&P=396830
Subject: Re: group DCM analysis without group GLM differences? From: James Rowe Date: Fri, 17 Oct 2008 21:17:39 +0100
11x) Nonlinear influences of area X on connection Y -> Z can only be assessed as condition-independent effects (not bilinear):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901&L=spm&F=&S=&P=268077
Subject: AW: non-linear DCM From: Klaas Enno Stephan Date: Tue, 13 Jan 2009 18:59:05 +0000
11y) How is directionality of causal influces of area z2 on area z1 encoded in DCM?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0901&L=spm&F=&S=&P=463722
Subject: Re: Direction of connectivities in DCM From: Karl Friston Date: Wed, 21 Jan 2009 15:43:38 +0000
11z) How is the information stored in the dcm.mat files in SPM8b?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=spm&F=&S=&P=692838
Subject: Re: 2 questions about DCM in SPM8b From: Maria Joao Date: Sat, 28 Mar 2009 13:57:20 +0000
11a1) How do you best report individual % increases or decreases in connectivity strengths?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=spm&F=&S=&P=561926
Subject: DCM: fixed vs. random effects BMS; direction of connectivity change From: Narender Ramnani Date: Fri, 22 May 2009 09:23:54 +0100
% increase or decrease in the fixed connectivity (A) implied by the condition specific effect (B):
100*DCM.Ep.B{i}(j,k)/DCM.EpA(j,k)
11b1) How do you best acquire fMRI data for DCM (continuous vs. interleaved)?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0906&L=spm&F=&S=&P=651514
Subject: Re: DCM From: Klaas Enno Stephan Date: Wed, 24 Jun 2009 16:51:29 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0907&L=spm&F=&S=&P=109049
Subject: Re: DCM - interleaved sequence From: Klaas Enno Stephan Date: Mon, 6 Jul 2009 16:49:51 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0909&L=spm&F=&S=&P=268521
Subject: Re: DCM - interleaved sequence From: Klaas Enno Stephan Date: Tue, 15 Sep 2009 08:55:00 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1209&L=spm&F=&S=&P=60980
Subject:Re: DCM course in Paris From:Hanneke den Ouden <[log in to unmask]> Date:Tue, 4 Sep 2012 16:31:23 +0200
11c1) Is DCM model selection based on positive evidence ratio (PER) still valid in SPM8?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0907&L=spm&F=&S=&P=154652
Subject: Re: problems of models selection From: Klaas Enno Stephan Date: Wed, 8 Jul 2009 09:26:54 +0000
11d1) How do you most appropriately use the new BMS model selection feature in SPM8?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0907&L=spm&F=&S=&P=472740
Subject: Re: DCM BMS results interpretation From: Klaas Enno Stephan Date: Wed, 22 Jul 2009 20:56:16 +0000
but see:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0907&L=spm&D=0&P=490430
Subject: Re: DCM BMS results interpretation From: Mohamed Seghier Date: Thu, 23 Jul 2009 13:17:36 +0100
and ...:
11e1) How do you perform a quicker BMS model selection without first creating DCM.mat files?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0909&L=spm&F=&S=&P=517010
Subject: Re: Log-evidence matrix in BMS From: Maria Joao Date: Thu, 24 Sep 2009 18:36:15 +0100
11f1) Questions about model family comparisons and BMS:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0910&L=spm&F=&S=&P=39111
Subject: Re: Questions about model family comparisons and BMS From: Klaas Enno Stephan Date: Sun, 4 Oct 2009 17:03:42 +0000 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=spm&F=&S=&P=251553 Subject: Re: DCM - choosing a model when there is no significant difference From: Klaas Enno Stephan Date: Mon, 8 Feb 2010 14:04:09 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1005&L=spm&F=&S=&P=16343
Subject: Re: model selection DCM From: Klaas Enno Stephan Date: Mon, 3 May 2010 10:24:01 -0700
11g1) Difference between Bayesian parameter averaging (BPA) and Bayesian model averaging (BMA):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0910&L=spm&F=&S=&P=267880
Subject: Re: Questions about model family comparisons and BMS From: Klaas Enno Stephan Date: Mon, 12 Oct 2009 19:04:06 +0000
11h1) DCM and sparse sampling?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0911&L=spm&F=&S=&P=601383
Subject: Re: DCM problem From: Klaas Enno Stephan Date: Tue, 24 Nov 2009 15:56:12 +0000
11i1) How do you find out whether the system is rather driven by area A or B?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1003&L=spm&F=&S=&P=216387
Subject: Re: DCM Driving Inputs From: Hanneke den Ouden Date: Tue, 9 Mar 2010 13:46:18 +0100
11k1) How meaningful it is to investigate DCM.A parameters in SPM?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1006&L=spm&F=&S=&P=240383
Subject: Re: Question concerning the A parameters in DCM From: Karl Friston Date: Fri, 11 Jun 2010 17:33:12 +0100
11l1) How do you reduce the model space to a manageable size based on a priori hypothesis?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1007&L=spm&F=&S=&P=237274
Subject: Re: Question on DCM Model search From: Klaas Enno Stephan Date: Mon, 12 Jul 2010 16:18:32 +0000
11m1) Can you specify an afferent connection from the same region receiving an input?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1007&L=spm&F=&S=&P=231661
Subject: Re: Defining a driving input for DCM in a self initiated task From: Klaas Enno Stephan Date: Mon, 12 Jul 2010 16:14:20 +0000
11n1) Are self-connections necessary in DCM SPM8?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1009&L=spm&F=&S=&P=146368
Subject: Re: DCM: self-connections From: Klaas Enno Stephan Date:Mon, 13 Sep 2010 09:54:25 -0700
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1204&L=spm&F=&S=&P=314868
Subject:Re: Does DCM require modulation of self connections? From:Mohamed Seghier Date:Mon, 16 Apr 2012 15:47:08 +0100
11o1) In how far does SPM10 differ from SPM8?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1011&L=spm&F=&S=&P=533582
Subject:Re: DCM10 From:Klaas Enno Stephan Date:Mon, 22 Nov 2010 18:47:52 +0000
11p1) What does the matlab error message “Matrix is close to singular or badly scaled” refer to?
Subject:Re: error message for DCM From:Klaas Enno Stephan Date:Fri, 17 Sep 2010 12:06:52 -0700
11q1) Comments on event-modulators and design efficiency?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1103&L=spm&F=&S=&P=525427
Subject:Re: DCM questions From:Klaas Enno Stephan Date:Sat, 19 Mar 2011 17:39:02 +0000
11r1) When using BMS, one should infer the most likely model by comparing the entire set of plausible models at once, instead of selectively analysing subparts of model space:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1006&L=spm&F=&S=&P=363420
Subject:Re: Second try: # of DCMs in BMS affects rank ordering From:Klaas Enno Stephan Date:Thu, 17 Jun 2010 08:46:52 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1104&L=spm&F=&S=&P=25923
Subject: Re: strange results in DCM model comparison, SPM8 From:Klaas Enno Stephan Date: Sun, 3 Apr 2011 10:25:45 +0100
11s1) Conditional dependencies (correlated regressors) in BMS and DCM:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1104&L=spm&F=&S=&P=93703
Subject:Re: DCM-Conditional Dependencies From:Klaas Enno Stephan Date:Wed, 6 Apr 2011 20:29:30 +0100
11t1) How much noise does DCM tolerate?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&F=&S=&P=113930
Subject:Re: Signal to Noise Ratio in DCM From:"Friston, Karl" Date:Fri, 3 Feb 2012 20:26:40 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;6441d0c9.1202
Subject: Re: Signal to Noise Ratio in DCM From:"Friston, Karl" Date:Mon, 6 Feb 2012 19:24:44 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;d0dd6cc4.1202
Subject:Re: Signal to Noise Ratio in DCM From:"Penny, William" Date:Mon, 6 Feb 2012 17:29:55 +0000
11u1) How do you create synthetic data within DCM?
spm8/spm_dcm_generate.m
Subject:Re: Signal to Noise Ratio in DCM From:"Friston, Karl" <[log in to unmask]> Date:Fri, 3 Feb 2012 20:26:40 +0000
11v1) How do you specify delays within slice-timed and non slice-timed DCM models?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&F=&S=&P=495050
Subject:Re: delays vector in DCM From:Hanneke den Ouden Date:Mon, 20 Feb 2012 18:41:09 -0500
11x1) Suggestions on finding best model in a large model space:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1203&L=spm&F=&S=&P=83132
Subject:Re: BMS:DCM:rfx From:"Penny, William" Date:Mon, 5 Mar 2012 16:44:09 +0000
11y1) Comments on the optimization of priors in DCM8 vs DCM10 vs DCM12 and explanations for the incosistent results between DCM versions and particularly for the “flat-lining” of effects in DCM10:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1203&L=spm&F=&S=&P=215052
Subject: From:"Friston, Karl" Date:Sun, 11 Mar 2012 14:09:40 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1203&L=spm&F=&S=&P=491468
Subject: From:Klaas Enno Stephan Date:Sat, 17 Mar 2012 10:05:45 +0000
Subject: From:Hanneke den Ouden Date:Wed, 28 Mar 2012 18:43:00 -0400
Subject:Re: Model flatlining: priors in DCM8, DCM10 From:Mohamed Seghier Date:Wed, 23 May 2012 11:25:00 +0100
11z1) Potential problem with DCM10 and short epochs (solved in DCM12):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;e0d295cf.1205
Subject:Scaling of Input to DCM for fMRI From:Rik Henson Date:Thu, 31 May 2012 19:04:11 +0000
11a2) What does the question “centre input” in DCM12 specification mean?
Subject:Re: specify models in DCM10 (SPM8) From:"Friston, Karl" Date:Sat, 17 Dec 2011 22:03:59 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;df32c9c1.1405
Subject:Re: Network Discovery with DCM From:"Zeidman, Peter" <[log in to unmask]> Date: Fri, 16 May 2014 15:01:35 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;b9abdfc2.1508
Subject:Re: DCM and centre input From:"Zeidman, Peter" Date:Fri, 21 Aug 2015 09:14:21 +0000
11b2) How to correct / adjust VOIs for the effects of interest?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1301&L=spm&F=&S=&P=464953
Subject:Re: mean correct parametric modulators for DCM? From:"Penny, William" Date:Tue, 29 Jan 2013 10:05:54 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;c45575d5.1405
Subject:Re: a basic DCM question From:"Zeidman, Peter" Date:Mon, 12 May 2014 09:40:26 +0000
11c2) How do you perform a simple VOI-based regression in SPM (including resting state)?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;47e6af.1303
Subject: Re: connectivity analysis - simple question concerning general procedure From: Dr Cyril Pernet Tue, 12 Mar 2013 11:39:42 +0000
11d2) How do you manually specify models with more than 8 VOIs/nodes?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1311&L=spm&F=&S=&P=11081
Subject: Re: DCM post-hoc analysis From:"Friston, Karl" Date:Fri, 1 Nov 2013 14:25:38 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1405&L=spm&F=&S=&P=532882
Subject:Re: DCM estimate and DCM posthoc: 2 questions From:"Zeidman, Peter" Date:Wed, 21 May 2014 13:35:30 +0000
→ see modified spm12b .m files with .nmax16 extension!
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1407&L=spm&F=&S=&P=626922
Subject:Re: DCM, max#VOI's From:"Zeidman, Peter" Date:Wed, 23 Jul 2014 10:00:35 +0000
11e2) Is there a possibility to refine model specification or estimation by additional prior regressors (such as anatomical connectivity values between regions)?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1311&L=spm&F=&S=&P=11170
Subject: Re: DCM post-hoc analysis From:"Friston, Karl" Date:Fri, 1 Nov 2013 14:25:38 +0000
11f2) How do you use DCM for resting state analysis?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;f16c9ac2.1401
Subject: Re: resting state fMRI data From:Adeel Razi Date:Mon, 20 Jan 2014 11:13:30 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1412&L=spm&F=&S=&P=77649
Subject:Re: DCM-fMRI From:"Zeidman, Peter" Date:Thu, 4 Dec 2014 11:03:59 +0000
11g2) How do you specify families for post-hoc optimization (network discovery)?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;1b3d6fbe.1404
Subject:Re: family partitions in DCM post-hoc From:"Zeidman, Peter" Date:Mon, 14 Apr 2014 10:25:45 +0000
11h2) Reduced model instead of full model as starting point for post-hoc optimization (network discovery):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1412&L=spm&F=&S=&P=95535
Subject:Re: DCM post hoc: specification of the "full" model From:"Zeidman, Peter" Date:Thu, 4 Dec 2014 16:51:30 +0000
11i2) How to interpret self-connections (and intrinsic connections) in DCM-SPM12:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1412&L=spm&F=&S=&P=255518
Subject:Re: DCM: How to interpret intrinsic connections values computed by DCM12 From:"Zeidman, Peter" Date:Mon, 8 Dec 2014 17:10:17 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;479d546e.1504
Subject: Re: 回复：RE: [SPM] question about DCM in SPM12: the value in mEp
From:"Zeidman, Peter"
Date:Thu, 16 Apr 2015 12:05:21 +0000
11j2) How do you define starting point parameters for DCM12 estimation?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;cca9fc1e.1412
Subject:Re: Two-state dcm does not converge From:"Zeidman, Peter" Date:Tue, 16 Dec 2014 13:11:28 +0000
11k2) How do you extract log evidence values from already inverted DCMs?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1501&L=spm&F=&S=&P=377024
Subject:Re: DCM - Log Evidence breakdown From:Mohamed Seghier Date:Tue, 20 Jan 2015 18:50:12 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1507&L=spm&F=&S=&P=534708
Subject:Re: DCM From:"Zeidman, Peter" Date:Thu, 23 Jul 2015 11:59:42 +0000
evidence = spm_dcm_evidence(DCM) ;
Accuracy =
sum(evidence.region_cost) ;
Complexity = Accuracy – DCM.F ;
11l2) How do you deal with parameters whose presence is suggested by model selection but which are non-significant in BMA?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;2e73d9ed.1502
Subject:Re: reporting DCM results From:"Zeidman, Peter" Date:Wed, 11 Feb 2015 09:26:20 +0000
11m2) How do you further investigate the optimum model of spm_dcm_post_hoc DCM Network Discovery (Bayesian Model Reduction (BMR))?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1503&L=spm&F=&S=&P=480448
Subject:Re: Network discovery using DCM Optimize From:"Zeidman, Peter" Date:Fri, 20 Mar 2015 11:47:40 +0000
11n2) How do you convert intrinsic connection matrix values to Hz units?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;392ee331.1504
Subject: Re: 回复：RE: [SPM] 回复：RE: [SPM] question about DCM in SPM12: the value in mEp From:"Zeidman, Peter" Date:Tue, 21 Apr 2015 13:24:03 +0000
11o2) How does the DCM post-hoc network discovery algorithm work?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1506&L=spm&F=&S=&P=836351
Subject:Re: DCM post-hoc Output From:"Zeidman, Peter" Date:Wed, 24 Jun 2015 15:06:01 +0000
11p2) Alternative to random-effects spm_dcm_post_hoc and follow-up probabilities extraction:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1509&L=spm&F=&S=&P=90076
Subject:Re: Questions about the post-hoc dcm analysis From:"Zeidman, Peter" Date: Wed, 9 Sep 2015 08:40:24 +0000
11q2) Specify a parameter that can't change in DCM:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;49568397.1510
Subject: Re: DCM options.P From:"Zeidman, Peter" Date:Wed, 28 Oct 2015 13:12:14 +0000
11r2) BMA and group comparisons:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1511&L=spm&F=&S=&P=117470
Subject:Re: DCM of two groups From:"Zeidman, Peter" Date:Thu, 5 Nov 2015 10:51:55 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;68dcdf1d.1511
Subject:Re: DCM BMA From:"Zeidman, Peter" Date:Fri, 6 Nov 2015 14:31:17 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1511&L=spm&F=&S=&P=196748
Subject:Re: DCM model evidence and free parameters From:"Zeidman, Peter" Date:Fri, 6 Nov 2015 17:25:23 +0000
11s2) How to perform between-groups comparisons through Parametric Empirical Bayes (PEB):
https://en.wikibooks.org/wiki/SPM/Parametric_Empirical_Bayes_%28PEB%29
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1706&L=spm&F=&S=&P=46430
Subject: Re: PEB From:"Zeidman, Peter" Date: Tue, 6 Jun 2017 07:45:44 +0000
see also, scoring a large number of models:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;23c74618.1801
Subject: Re: max number of DCMs (for fMRI)? From:"Zeidman, Peter" Date:Tue, 30 Jan 2018 09:53:25 +0000
11t2) What is the most frequent outcome of modelling learning (post vs pre) effects in DCM?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1801&L=spm&F=&S=&P=214788
Subject:Re: DCM for test-retest (longitudinal) fMRI experiment From:"Friston, Karl" Date:Fri, 19 Jan 2018 17:49:49 +0000
12a) How do you check for VBM segmentation quality?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&O=D&F=&S=&P=122717
Date: Mon, 21 Mar 2005 09:46:35 -0500 From: "Meyer-Lindenberg, Andreas (NIH/NIMH)" Subject: Re: VBM segmentation quality
12b) Do you better use FWE or FDR correction for VBM analysis?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=6693514
Date: Thu, 21 Dec 2006 19:17:37 +0000 From: Ged Ridgway Subject: Re: VBM: FDR vs. FWE (cf. cluster size inference)
12c) What is the optimal level of bias correction in SPM8 segmentation?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=SPM&D=1&T=0&O=D&P=211317
Subject: Re: bias correction - what level? From: Dana Perantie Date: Fri, 22 May 2009 16:27:07 -0500
12d) Guidelines for an “optimal” VBM procedure in SPM8 (SPM5):
http://en.wikibooks.org/wiki/SPM/VBM#Unified_Segmentation_in_SPM5
http://keck.ucsf.edu/~schenk/SPM5Tutorial/
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0904&L=SPM&P=R62362&m=35118
Subject: Re: Multispectral segmentation in spm8 From: John Ashburner Date: Wed, 15 Apr 2009 11:48:55 +0000
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0905&L=SPM&P=R47463&m=36196
Subject: Re: DARTEL & New Segmentation in SPM8 From: John Ashburner Date: Wed, 20 May 2009 11:17:34 +0000
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0905&L=SPM&P=R18196&m=36196
Subject: Re: VBM IN SPM8? From: Christian Gaser Date: Wed, 13 May 2009 15:17:38 +0100
https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0905&L=SPM&P=R18140&m=36196
Subject: Re: VBM IN SPM8? From: Christian Gaser Date: Wed, 13 May 2009 15:12:01 +0100
Very useful! https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0907&L=SPM&T=0&O=D&P=3605
Subject: Re: SPM VBM Inquiries From: Guillaume Flandin Date: Wed, 1 Jul 2009 14:34:07 +0100
12e) How to set and increase the absolute threshold for VBM analyses:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1005&L=SPM&D=1&O=D&P=232175
Subject: Re: A question about vbm8 toolbox.. From: Christian Gaser Date: Thu, 27 May 2010 06:48:51 +0100
12f) When is it necessary to correct for Total Intracranial Volume (& other useful indications)?
Subject:Re: DARTEL-VBM: total intracranial volume in second level analysis From:"MCLAREN, Donald" Date:Mon, 7 Feb 2011 11:53:21 -0500
How to calculate Total Intracranial Volume:
http://dbm.neuro.uni-jena.de/vbm/segmentation/modulation/
or:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0701&L=SPM&P=R10670
Subject: Re: VBM question From:"Ashburner John” Date:Wed, 10 Jan 2007 10:41:45 +0100
12g) Notes on when a customized template is still needed in the SPM8 Segmentation/Dartel approach:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1103&L=SPM&F=&S=&P=304816
Subject:Re: Question about making tissue probability maps From:John Ashburner Date:Mon, 28 Mar 2011 15:01:35 +0100
12h) How do you perform image skull stripping in SPM?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;19d2e241.1202
Subject:Re: skull strip From:Christian Lambert Date:Tue, 14 Feb 2012 12:33:43 +0000
12i) Important notes on the VBM8 integration with SPM8 NewSegmentation and DARTEL:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;f0f4c93e.1104
Subject: Re: VBM8 integration with DARTEL From:Christian Gaser Date: Tue, 12 Apr 2011 08:50:44 +0100
12j) Longitudinal VBM
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;2f68e1e5.1403
Subject:Re: Longitudinal VBM using Longitudinal Registration in SMP12b From:John Ashburner Date:Fri, 28 Mar 2014 13:47:34 +0000
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406&L=spm&D=0&P=561309
Subject:Re: Globals in longitudinal VBM From:DRC SPM Date:Tue, 24 Jun 2014 09:15:53 +0100
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;33cc704c.1406
Subject:Re: Using longitudinal registration for VBM - effect of time difference From:DRC SPM Date:Tue,24 Jun 2014 09:52:31 +0100
12k) Interpretation of modulated VMB measures as volume or density of gray matter:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1510&L=spm&D=0&P=756352
Subject:Re: Terminology debate: GM Volume vs Density From:Christian Gaser Date:Thu, 29 Oct 2015 07:28:32 +0000
13a) Is it wise to analyze together DTI images acquired with different slice numbers?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;7cb08b89.1009
Subject: Re: DTI processing with different slices From: "S.F.W. Neggers" Date: Fri, 17 Sep 2010 14:53:49 +0200
13b) How do you check DTI image quality?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;34470f4a.1010
Subject:Re: DTI data quality checking From:Michel Thiebaut de Schotten Date:Fri, 8 Oct 2010 09:34:23 +0200
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;feffaa27.1010
Subject: DTI data quality checking From: Volkmar Glauche
Date: Fri, 8 Oct 2010 12:04:31 +020013a) How do ru
13c) Is it better to analyze FA in SPM or SnPM?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1010&L=SPM&O=D&P=123769
Subject: Re: Empirical extent threshold for voxel based analysis From: Michel Thiebaut de Schotten Date: Wed, 13 Oct 2010 20:40:14 +0200
14a) How do run a batch file from the command line in SPM5?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind05&L=spm&O=D&F=&S=&P=451633
Date: Thu, 8 Dec 2005 18:03:02 +0100
From: Volkmar Glauche
Subject: Re: SPM5 batch
14b) How do inspect a batch .mat jobs from matlab?
e.g. for 1st level statistical models:
>> jobs{1}.tools{1}.rwls{1}.fmri_rwls_spec
or for spatial preprocessing:
>> jobs{1}.spatial{1}.realign{1}.estwrite
alternatively:
>> jobs{1}.
then press <tab> key to complete (>> jobs{1}.tools{1}. ecc.)
14c) How do you edit a batch file in SPM5 with a standard text editor?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0805&L=spm&O=D&F=&S=&P=13238
Date: Sat, 10 May 2008 17:57:18 +0200 From: Volkmar Glauche Subject: Re: Question on batching preprocessing
14d) How do you run SPM5 without graphic output?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=5715560
Date: Wed, 1 Nov 2006 10:54:50 -0600 From: "Senjem, Matthew L. [RO IMAGNG]" Subject: Re: running without GUI
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0703&L=spm&F=&S=&P=454177
Date: Thu, 22 Mar 2007 15:08:14 +0100 From: Jérôme Redouté Subject: Re: using SPM5 without GUI
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0703&L=spm&F=&S=&P=458689
Date: Thu, 22 Mar 2007 15:24:38 +0000 From: Christian Gaser Subject: Re: using SPM5 without GUI
14e) Toward a batch interface for SPM5...
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0612&L=spm&O=D&F=&S=&P=35254
Date: Thu, 28 Dec 2006 13:03:11 -0600 From: Darren G Subject: Re: multiple conditions feature of SPM5
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0612&L=spm&O=D&F=&S=&P=35491
Date: Thu, 28 Dec 2006 21:43:43 +0100 From: Volkmar Glauche Subject: Re: multiple conditions feature of SPM5
14f) How do you set up a batch script in SPM5 to define a set of contrasts?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0703&L=spm&O=D&F=&S=&P=17902
Date: Mon, 12 Mar 2007 10:47:28 -0700 From: Paul Macey Subject: Re: Setting up contrasts from command line? --> vedi file /mnt/hda5/work/spm/batch/make_contrast_SPM5.m
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0703&L=spm&O=D&F=&S=&P=18017
Date: Mon, 12 Mar 2007 18:47:43 +0100 From: Volkmar Glauche Subject: Re: Setting up contrasts from command line?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0703&L=spm&O=D&F=&S=&P=18403
Date: Mon, 12 Mar 2007 20:40:05 +0000 From: Thomas Nichols Subject: Re: Setting up contrasts from command line? --> vedi files /mnt/hda5/work/spm/batch/MakeCon_TNichols.m /mnt/hda5/work/spm/batch/example_Cspec_TNichols.m
or in SPM2 style:
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709&L=spm&O=D&F=&S=&P=2853
Date: Wed, 5 Sep 2007 10:43:25 +0200 From: Christian Büchel Subject: AW: [SPM] Is it possible to enter t contrasts collectively?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709&L=spm&O=D&F=&S=&P=2723
Date: Wed, 5 Sep 2007 09:24:18 +0100 From: Alexa Morcom Subject: Re: Is it possible to enter t contrasts collectively?
14g) How do you run multiple subjects batches in SPM5?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0703&L=spm&O=D&F=&S=&P=21483
Date: Wed, 14 Mar 2007 07:14:19 +0000 From: Markus Burgmer Subject: Re: SPM5 batch preprocessing
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0703&L=spm&O=D&F=&S=&P=23326
Date: Thu, 15 Mar 2007 11:19:08 +0100 From: "Juanjo Lull (UPV)" Subject: Re: SPM5 batch preprocessing
14h) Flexible batch scripts in SPM8...
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0812&L=spm&D=1&T=0&O=D&P=453
Subject: Re: Automating normalizations (and other operations) From: Volkmar Glauche Date: Mon, 1 Dec 2008 11:19:49 +0100
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=SPM&D=1&T=0&O=D&P=13218
Subject: Re: soft paths in batch mode From: Volkmar Glauche Date: Wed, 1 Apr 2009 22:08:22 +0200
14i) ... and conversion of batch scripts from SPM5 to SPM8
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0904&L=SPM&D=1&T=0&O=D&P=34771
Subject: Re: question about batch mode in spm8 From: Volkmar Glauche Date: Fri, 3 Apr 2009 08:37:55 +0200
14j) How do you insert a module within an already created batch file?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=SPM&D=1&T=0&O=D&P=179941
Subject: Re: batch editor SPM8 From: Volkmar Glauche Date: Mon, 15 Feb 2010 14:12:04 +0100
answer to:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1002&L=SPM&D=1&T=0&O=D&P=177525
Subject: batch editor SPM8 From: Fabien GIERSKI Date: Mon, 15 Feb 2010 12:33:02 +0100
14k) How do yousave a copy of a job with all dependencies replaced by actual values?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1103&L=SPM&T=0&O=D&P=9021
Subject:matlabbatch "decode dependencies" From:Volkmar Glauche Date:Tue, 1 Mar 2011 16:36:01 +0100
15. SPM functions, Toolboxes & Miscellaneous
15a) How do you use file name filtering with spm_select in SPM5?
>> help regexp
spm_select(Inf,'image','Select Image',[],pwd,'test*')
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0612&L=spm&O=D&F=&S=&P=9879
Date: Thu, 7 Dec 2006 17:52:45 +0100 From: Volkmar Glauche Subject: Re: Filtering in spm_select
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0612&L=spm&O=D&F=&S=&P=10002
Date: Thu, 7 Dec 2006 16:55:51 +0000 From: Ged Ridgway Subject: Re: Filtering in spm_select
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0612&L=spm&O=D&F=&S=&P=10106
Date: Thu, 7 Dec 2006 11:56:10 -0500 From: Fabio Sambataro Subject: Re: Filtering in spm_select
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0612&L=spm&O=D&F=&S=&P=13590
Date: Fri, 8 Dec 2006 16:53:47 +0000 From: Ged Ridgway Subject: Re: Filtering in spm_select
15b) How do you apply the same formula to each image of a matrix of n images with SPM5 ImCalc?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0808&L=spm&T=0&O=D&P=31066
Subject: Re: Imcalc SPM5 batch?
From: "Vince D. Calhoun"
Date:Mon, 25 Aug 2008 21:20:41 -0600http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0808&L=spm&D=1&T=0&O=D&P=33301
From: "Jeff Browndyke, Ph.D." Reply-To: Jeff Browndyke, Ph.D. Date: Tue, 26 Aug 2008 21:18:31 -0400
15c) How do you map a single voxel from source space to target space (e.g. coregistered)?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0702&L=spm&O=D&F=&S=&P=38249
Date: Thu, 22 Feb 2007 13:51:48 +0100 From: "Ashburner John (PSYCHOLOGY)" Subject: Re: applying normalisation parameters to individual voxels
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0702&L=spm&O=D&F=&S=&P=36372
Date: Wed, 21 Feb 2007 13:19:11 +0000 From: Ged Ridgway Subject: Re: applying normalisation parameters to individual voxels
15d) How do you map a single voxel from the MNI space to the native subject space?
SPM5 > TASKS > Util > Deformations
- Deformations
+ composition
New imported _sn.mat
Parameter File -> _sn.mat (generated by segmentation or normalisation: not inv_sn.mat!!)
Voxel sizes & Bbox: leave empty
Save as: deformation_sn (creates: y_deformation_sn.nii)
Apply to: leave empty
In matlab:
>> P=spm_select(1,'image','Select deformation'); % select y_deformation_sn.nii
>> P=[repmat(P,3,1) [',1';',2';',3']];
>> V=spm_vol(P);
>> norm_mm = [-38 -52 51];% mm co-ordinate in MNI space
>> norm_vox = V(1).mat\[norm_mm 1]';
>> xyz = [0 0 0];
>> xyz(1) = spm_sample_vol(V(1),norm_vox(1),norm_vox(2),norm_vox(3),1);
>> xyz(2) = spm_sample_vol(V(2),norm_vox(1),norm_vox(2),norm_vox(3),1);
>> xyz(3) = spm_sample_vol(V(3),norm_vox(1),norm_vox(2),norm_vox(3),1);
>> fprintf('Co-ordinates are %g,%g,%g\n',xyz(1),xyz(2),xyz(3)); % prints mm co-ordinate in native subject space.
May have changed with DARTEL, see:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;79b328b5.1202
Subject:Re: Inverse normalize a coordinate in DARTEL from MNI to functional space From:Will Moore Date: Tue, 28 Feb 2012 21:07:40 -0800
Also see:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1304&L=spm&F=&S=&P=89382
Subject:Re: inverse transform of the coordinates of a single voxel From: "Neggers, S.F.W." Date: Wed, 3 Apr 2013 22:02:55 +0000
spm8/spm_get_orig_coord.m
And more recently:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;8005badf.1606
Subject: Re: how to get the individual coordinate from the MNI space From: John Ashburner Date:Wed, 1 Jun 2016 14:56:37 +0100
Py = 'y_blah.nii';
Pnative = 'blah.nii';
% mm coordinate in MNI space (right hippo).
xyz_mni = [29 -19 -18];
% voxel coordinate in MNI space of y_*.nii
Nii = nifti(Py);
iM = inv(Nii.mat);
ijk = iM(1:3,:)*[xyz_mni 1]';
% mm coordinate in native images
native_x = spm_bsplins(Nii.dat(:,:,:,1,1),ijk(1),ijk(2),ijk(3),[1 1 1 0 0 0]);
native_y = spm_bsplins(Nii.dat(:,:,:,1,2),ijk(1),ijk(2),ijk(3),[1 1 1 0 0 0]);
native_z = spm_bsplins(Nii.dat(:,:,:,1,3),ijk(1),ijk(2),ijk(3),[1 1 1 0 0 0]);
% voxel coordinate in native image Pnative
Nii_image = nifti(Pnative);
iM2 = inv(Nii_image.mat);
ijk_native = iM2(1:3,:)*[native_x native_y native_z 1]'
15e) How do extract the time courses from all voxels?
You need to call spm_read_vols on V to read all data from all voxels and all volumes.
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0712&L=spm&O=D&F=&S=&P=293
Date: Sun, 2 Dec 2007 18:42:18 +0100 From: Volkmar Glauche Subject: Re: which one has the information of time courses?
15f) How do you convert voxel coordinates from ICBM to Talairach space (apart from Brett's mni2tal)?
http://www.brainmap.org/icbm2tal/index.html
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0712&L=SPM&T=0&O=D&P=15042
Date: Tue, 4 Dec 2007 15:25:33 -0500 From: Benjamin Wagner Subject: Re: Coordinates difference between WFU_PickAtlas and icbm_spm2tal
but see:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0906&L=SPM&T=0&O=D&P=10778
Subject: Re: Converting MNI coordinates, which tool? From: Matthew Brett Date: Mon, 1 Jun 2009 14:40:49 -0400
15g) How do you switch from an SPM5 to an SPM8 session or viceversa?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=SPM&T=0&O=D&P=51879
Subject: Re: running SPM5 and SPM8 From: Guillaume Flandin Date: Wed, 6 May 2009 13:34:55 +0100
15h) Are there any alternatives to Julich's cytoarchitectonic maps for probabilistic anatomical mapping?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0907&L=SPM&D=1&T=0&O=D&P=57449
Subject: Re: Is there any map converting MNI to Brodmann area? From: "Hammers, Alexander" Date: Wed, 8 Jul 2009 10:29:06 +0100
15i) How do you generate cortical flat maps in SPM8?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0908&L=SPM&F=&S=&P=123532
Subject: Re: 3d surface flattening From: Torben Ellegaard Lund Date: Thu, 6 Aug 2009 11:08:35 +0200
15j) Tips on how to create custom renderings:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0912&L=SPM&D=1&T=0&O=D&P=129851
Subject: Re: spm8 surface rendering and cortex_20484_surf.gii From: Guillaume Flandin Date: Mon, 14 Dec 2009 21:22:01 +0000
15k) How do you “read data into data matrix" to calculate a mean image with ImCalc without specifying the formula:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1103&L=SPM&F=&S=&P=726812
Subject: Re: ImCalc From: Torben Ellegaard Lund Date: Tue, 22 Mar 2011 18:59:36 +0100
15l) Tool for power calculation supporting SPM and multiple comparison problem:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1106&L=SPM&F=&S=&P=324862
Subject:Re: power calculation tool for SPM users From:Jeanette Mumford Date:Wed, 15 Jun 2011 11:34:57 -0500
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1212&L=spm&F=&S=&P=407912
Subject:Re: Sample Size calculations - AGAIN From:Mehul Trivedi Date:Thu, 20 Dec 2012 16:07:43 +0000
15m) How do you project SPM activation maps onto Freesurfer cortical renderings?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&F=&S=&P=693170
Subject:Re: SPM8 results onto freesurfer surfaces From:"MCLAREN, Donald" Date:Tue, 28 Feb 2012 13:38:15 -0500
15n) Matlab scripts to expand and collapse 4D nii scans:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1202&L=spm&F=&S=&P=726374
Subject:Re: ArtRepair toolbox compatibility with nii images From:"MCLAREN, Donald" Date:Wed, 29 Feb 2012 18:26:36 -0500
Adapted for my own purposes and stored as:
/usr/local/spm/add_ons/nifti4D_to_vols3D.m
/usr/local/spm/add_ons/vols3D_to_nifti4D.m
(use with caution!)
→ see instead 16v) for a more convenient solution!
15o) How do you improve default mode network identification with ICA (Gift Toolbox):
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1205&L=spm&F=&S=&P=556661
Subject:TRe: [SPM] default mode network From:"Vince D. Calhoun" Date:Fri, 18 May 2012 22:51:32 +0000
15p) How do you create ROI masks (e.g. AAL), label regions, and average signal in ROIs in SPM12?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1504&L=spm&F=&S=&P=275160
Subject:Re: AAL and DCM From:Guillaume Flandin Date:Tue, 14 Apr 2015 17:33:47 +0100
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;9bb033a.1504
Subject:Re: Parcellation code From:Guillaume Flandin Date:Wed, 15 Apr 2015 14:53:07 +0100
15q) How do you apply a mask to a 4D image file in SPM12?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1607&L=spm&F=&S=&P=27633
Subject:Re: Imcalc From:Torben Lund Date:Mon, 4 Jul 2016 12:34:43 +0200
>> spm_mask
15r) How do you get localization proportions (%) for voxels and clusters in neuromorphometrics?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;4103d511.1701
Subject:Re: Neuromorphometrics From:Guillaume Flandin Date:Mon, 23 Jan 2017 10:59:35 +0000
15s) How do you extract neuromorphometrics labels for all peak coordinates?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;653daefc.1701
Subject:Re: Neuromorphometrics From:Guillaume Flandin Date:Tue, 24 Jan 2017 10:29:50 +0000
xA = spm_atlas('load','neuromorphometrics');
XYZmm = [TabDat.dat{:,end}];
label = {};
for i=1:size(XYZmm,2)
label{i} = spm_atlas('query',xA,XYZmm(:,i));
end
open label
16. SPM, Matlab & Linux tricks
16a) How do you search for all available spm functions?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0602&L=spm&O=D&P=542
use the 'lookfor' matlab function
or: http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0602&L=spm&O=D&P=2588
list = depfun('file_name') creates a cell array of strings containing the paths of all the files that file_name.m uses
16b) How do you calculate the power spectrum of the canonical HRF?
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0104&L=spm&P=R27646&I=3
16c) How do you recover stimulus onset information from the SPM.mat file?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0801&L=SPM&F=&S=&P=285726
Date: Fri, 11 Jan 2008 16:40:52 -0800 From: Jan Gläscher Subject: Re: Can I look at the stimulus function from SPM?
16d) How do you make the red cross disappear from the glass brain view?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0602&L=spm&O=D&P=1911
For SPM2, yes. Here's a snippet that will do that
ha = findobj('Tag','hMIPax');
hp = get(ha,'UserData');
set(hp.hXr,'Visible','off')
to turn it back on
set(hp.hXr,'Visible','on')
16e) How do you make the crosshair disappear from the “sections” view in SPM5?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=SPM&P=R212151&I=-3
Date: Thu, 27 Apr 2006 14:55:33 +0200 From: Volkmar Glauche Subject: Re: Q: Orthogonal view
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind00&L=SPM&P=R139959&I=-3
Date: Wed, 16 Aug 2000 08:30:34 -0500 (CDT) From: "Darren Gitelman" Subject: Re: crosshairs
16f) How do you calculate the voxel-wise standard deviation (SD) of image file?
http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0602&L=spm&O=D&P=29189
16g) How do you plot the movement parameters from your rp_*.txt file?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind06&L=spm&F=&S=&P=2181688
Subject:Re: Realignment Parameters Plot From:Thomas Stephan Date:Thu, 11 May 2006 08:30:53 +0100
(see /media/sda3/Work/spm/add_ons/MT_matlab_scripts/rp_concatenation.m.txt)
P=load 'name of your txt file something like rp_blabla.txt';
%for the traslation parameters:
figure;plot(P(:,1:3));
%for the rotation parameters:
plot(P(:,4:6));
16h) How do you calculate the standard deviation of image files?
FSL: http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0602&L=spm&O=D&P=36274
matlab: http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0602&L=spm&O=D&P=36526
16i) How do you load the matrix of image values in matlab?
>> img = spm_read_vols(spm_vol('filename.img'));
or with coordinates:
>> [img XYZ] = spm_read_vols(spm_vol('filename.nii'));
or just header infos:
>> V = spm_vol('filename.nii');
16j) How do you calculate design variance?
DesVar = ctrs'*inv(SPM.xX.X'*SPM.xX.X)*ctrs
16k) How do you calculate standard error (i.e. (1/Efficiency)^0.5)?
StErr = trace(ctrs'*inv(SPM.xX.X'*SPM.xX.X)*ctrs)^0.5
16l) How do you calculate Efficiency?
Eff = trace(ctrs'*inv(SPM.xX.X'*SPM.xX.X)*ctrs)^-1
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0410&L=spm&P=R42150&I=3
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0104&L=spm&P=R32917&I=3
or: (http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0508&L=spm&O=D&F=&S=&P=40062)
% define your contrast of interest
contrast = ;
load SPM
Var = contrast'*SPM.xX.Bcov*contrast;
E = 1/Var
see also: http://www.math.mcgill.ca/keith/fmristat/#effic
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=SPM&D=0&O=D&T=0&P=244570
Subject: Re: modeling compound events From: Michael T Rubens Date: Sun, 29 Mar 2009 15:36:29 -0700
or: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1305&L=spm&F=&S=&P=510758
Subject: Calculating design efficiency From: James Lee Date: Mon, 20 May 2013 09:51:30 -0600
X=SPM.xX.X;
c=[1 -1 0];
disp( 1 / (c*inv(X'*X)*c' ) );
16m) How do you calculate correlation coefficients?
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0408&L=spm&P=R3305&I=3
corrcoef([SPM.xX.X(:,1) SPM.xX.X(:,10)]) prior to any whitening and high-pass filtering
corrcoef([SPM.xX.xKXs.X(:,i) SPM.xX.xKXs.X(:,j)]) whitened and filtered
16n) How do you set up a design matrix simulation?
>> figure % opens a graphic window
rest=[ones(1,10) zeros(1,10)];
rest=[rest rest rest rest rest]; %sets up rest boxcar (100 TR, 5 epochs, each 10 TR's long)
stim=[zeros(1,10) ones(1,10)];
stim=[stim stim stim stim stim]; % stimulation boxcar
X=zeros(100,3);
X(:,1)=rest';
X(:,2)=stim';
X(:,3)=1; % sets up the design matrix
imagesc(X) % view design matrix
colormap(gray);
16o) How do you get all beta values from a beta image (e.g. for correlation with some parameters)?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0906&L=SPM&D=1&T=0&O=D&P=64738
Subject: Re: beta value From: Vadim Axel Date: Sun, 7 Jun 2009 18:10:52 +0300 16p) How do you perform multiple file renaming in linux? To rename e.g. file1.nii, file2.nii ... file10.nii one would e.g. Run mmv "file[0-9].nii" "file0#1.nii" and end up with file01.nii, file02.nii... https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0907&L=SPM&T=0&O=D&P=176308 Subject: Re: strange question From: Volkmar Glauche Date: Tue, 21 Jul 2009 16:52:41 +0200
16q) How do you manually orthogonalize regressors? put your regressors in a matrix X1 in the order you want them to be orthogonalized and then use X2 = spm_orth(X1) https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0908&L=spm&F=&S=&P=219580 Subject: Re: Orthogonalization of regressors in SPM5 From: cyril pernet Date: Mon, 10 Aug 2009 12:07:49 +0100 16r) How do you improve speed and performance in SPM? https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;863a049c.1105 Subject: Re: Sold State Drives From: Torben Ellegaard Lund Date: Thu, 19 May 2011 15:40:11 +0200 16s) How do you know with which matlab functions the SPM GUI buttons are associated? https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1109&L=spm&F=&S=&P=654508 Subject: Re: command for getting spm functions From:Clifford Workman Date: Tue, 27 Sep 2011 10:38:33 -0400
>> guide spm_Menu.fig
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1611&L=spm&F=&S=&P=802613
Subject:Re: Finding out which file is called from the GUI From:Guillaume Flandin Date:Wed, 16 Nov 2016 11:47:23 +0000
Type the following before executing a batch:
> dbstop in matlabbatch/private/cfg_run_cm at 18
Then execute the batch of interest and when MATLAB stops, type:
> functions(cm.prog)
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;54829621.1611
Subject:Re: Finding out which file is called from the GUI
From:Guillaume Flandin
Date:Thu, 17 Nov 2016 16:29:33 +0000
> cfg_util('dbstop',1,1); % for job 1, module 1
16t) How do you check the SPM version?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1403&L=spm&D=0&P=590983
Subject:Re: Reference for SPM12b
From:Marko Wilke
Date: Mon, 24 Mar 2014 08:37:29 +0100
[v, r] = spm('ver')(see also other commands in the FORMAT specifications help header of the spm.m file)
16u) How do you discard a/more volume/s from within a 4D time series?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1403&L=spm&F=&S=&P=787573
Subject:Re: 4D mean.nii obtained with realignment From:Guillaume Flandin Date:Thu, 27 Mar 2014 14:58:46 +0000
16v) How do you parallelise FSL in neuro-debian?
http://neuro.debian.net/blog/2012/2012-03-09_parallelize_fsl_with_condor.html
see also: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1003&L=FSL&D=0&P=309661
Subject: Re: randomise_parallel defragment script not working From: James Coxon Date: Tue, 23 Mar 2010 17:02:01 +0100
16w) How do you inspect 4D time series in SPM12 (movie)?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1502&L=spm&F=&S=&P=411689
Subject: Re: huge chunk missing from glass brain after first level specification From: John Ashburner Date: Fri, 20 Feb 2015 09:34:31 +0000
16x) How do you open a matlab .fig file from the command line?
> hgload('file.fig')
16y) How do you display a gifti .gii file in spm (and test for openGL functionality)?
> spm_mesh_render
16y) How do you create a high-quality surface glass brain image?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1802&L=spm&F=&S=&P=67310
Subject:Re: glass brain with ROI spheres From:Medical University of Vienna Date:Fri, 2 Feb 2018 17:26:35 +0100
17a) How do you classify an event-related design with soas not aligned to volume onsets?
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2012q4/002290.html
From: debian at onerussian.com (Yaroslav Halchenko) Date: Thu, 11 Oct 2012 10:10:18 -0400 Subject: [pymvpa] rapid event-related design / beta series approach
For rapid event-related designs (soa < 5s), see http://dx.doi.org/10.1016/j.neuroimage.2011.08.076
Even more useful:
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2014q4/002935.html
From: Brian Murphy brian.murphy at qub.ac.uk Date: Tue Nov 18 18:37:12 UTC 2014 Subject: Previous message: [pymvpa] Event-related designs - Is the modeling of the HRF not recommened?
http://dx.doi.org/10.1016/j.neuroimage.2010.05.051
17b) Instructions on the proper use of map2nifti() , if you get an error “AttributeError: 'DatasetAttributesCollection' object has no attribute > 'mapper'”
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2013q4/002588.html
From: Yaroslav Halchenko debian at onerussian.com Date: Sat Nov 2 15:02:25 UTC 2013 Subject: [pymvpa] Help with map2nifti()
17c) How to orient the choice of the classifier and preprocessing, based on experiment design:
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2015q1/003058.html
[pymvpa] Question about classifiers Nick Oosterhof n.n.oosterhof at googlemail.com Sun Mar 29 16:01:26 UTC 2015
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2015q1/003060.html
[pymvpa] Question about classifiers Yaroslav Halchenko debian at onerussian.com Mon Mar 30 01:09:30 UTC 2015
17d) Notes on unbalanced data sets:
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2015q2/003100.html
[pymvpa] Unbalanced Datasets Bill Broderick billbrod at gmail.com Fri Apr 17 15:37:49 UTC 2015
17e) Permutation testing for searchlights:
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2015q2/003140.html
[pymvpa] Searchlights and Permutation testing Christopher J Markiewicz effigies at bu.edu Tue Jun 16 21:42:54 UTC 2015
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2015q3/003199.html
[pymvpa] Permutation testing and Nipype Bill Broderick billbrod at gmail.com Tue Aug 11 16:00:38 UTC 2015
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2015q3/003202.html
[pymvpa] Searchlight statistical inference Yaroslav Halchenko debian at onerussian.com Tue Aug 11 21:13:59 UTC 2015
17f) Representation Similarity Analysis
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2017q2/003628.html
[pymvpa] outputting p-values from searchlight Nick Oosterhof n.n.oosterhof at googlemail.com Fri May 19 14:04:26 UTC 2017
http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/2017q2/003632.html
[pymvpa] outputting p-values from searchlight William Graves william.wyatt.graves at gmail.com Fri May 19 14:47:37 UTC 2017