[Freesurfer] fsfast selxavg-sess error
hi i am going over the fsfast tutorial. i have completed all steps up to FsFastTutorial/905 Average session-level data by condition https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20session_2dlevel_20data_20by_20condition when i run selxavg-sess -sf sessid -df sesspar -analysis sem_assoc, i get the following error: ??? Undefined function or variable 'MRIread'. Error in == /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 160 == rstd = MRIread(instem,1); ??? Undefined function or variable 'r'. quiting matlab -- ERROR: fast_selxavg() failed\n ERROR (/autofs/space/engram_012/users/pman/bert-functional): selxavg failed can you please tell me why i am getting this error? thanks paymon hosseini ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fsfast selxavg-sess error
Add the following lines to your startup.m file
FSH = getenv('FREESURFER_HOME');
fshmatlab = sprintf('%s/matlab',FSH);
path(path,fshmatlab);
clear fshmatlab;
Paymon Hosseini wrote:
hi
i am going over the fsfast tutorial. i have completed all steps up to
FsFastTutorial/905 Average session-level data by condition
https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20session_2dlevel_20data_20by_20condition
when i run selxavg-sess -sf sessid -df sesspar -analysis sem_assoc,
i get the following error:
??? Undefined function or variable 'MRIread'.
Error in == /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m
On line 160 == rstd = MRIread(instem,1);
??? Undefined function or variable 'r'.
quiting matlab
--
ERROR: fast_selxavg() failed\n
ERROR (/autofs/space/engram_012/users/pman/bert-functional): selxavg
failed
can you please tell me why i am getting this error?
thanks
paymon hosseini
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] tksurfer - view - information - distance
It's the screen distance from the cursor or point clicked to the vertex it's reporting as the one the mouse is over or clicked. On Mon, Apr 10, 2006 at 02:09:25PM -0400, anthony gallo wrote: tksurfer - view - information - distance what is the reference point for this command, ie when the cursor is on point x with a value of, say 0.02 what is that the distance of? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] regarding mkanalysis-sess.new and brainmasks
I usually set it to about 20 sec (the interpretation of this parameter is that the temporal autocorrelation will return to 0 beyond this spacing). The brain mask is used to restrict the voxels overwhich the autocorrelation is computed and averaged (don't want to include air voxels in the computation). What do you mean that you see non-uniform values in the sig volume? Sebastian Moeller wrote: Hi All, as the subject line reveals, I have a question regarding mkanalysis-sess.new (running centos4_x86_64 3.0.1 pub stable, on SuSE 9.3, not that it matters...). My question is, is there any heuristic how to chose the -taumax parameter, that can be used in combination with a brainmask? I am wondering as the example usage from the fsfast workflow specifies a brainmask, but does not set -taumax, is that a useful approach? One more question about the brainmask I have is, (at least without a specified taumax) I still see non-uniform values in the sig volume, while actually expecting close to nothing, but I guess I have not groked how the masking is supposed to work... I would be happy for any pointers about this issue. And while on the matter, is there a way to allow empty conditions, i.e. use a sparse condition numbering in the .para files (trading the check for missing conditions versus the possibility to use stable identifiers for loads of conditions used over different days). Ahoi Sebastian -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Short Course in fMRI, Spring 06
Mark Vangel and I are offering a short course in the statistical signal processing of fMRI again. April 26 27, 2006 7th Floor Auditorium Building 149 Charlestown Navy Yard Free, but limited to 40 attendees. Register at: http://www.nmr.mgh.harvard.edu/martinos/training/shortCoursefMRIStats.php doug -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Recommendation for Linux machine
Hi, We plan to buy Linux machine for freesurfer and other brain image processing. Any recommendation and related links? Thanks Chunchun ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] regarding mkanalysis-sess.new and brainmasks
Hi Doug, hi List, On 10. Apr 2006, at 20:28 Uhr, Doug Greve wrote: I usually set it to about 20 sec (the interpretation of this parameter is that the temporal autocorrelation will return to 0 beyond this spacing). The brain mask is used to restrict the voxels overwhich the autocorrelation is computed and averaged (don't want to include air voxels in the computation). What do you mean that you see non-uniform values in the sig volume? Mmh, I was expecting that all the voxels outside the brainmask would not take part in the analysis/calculation at all, or that all the non_brain voxels in the sig_NNN.bfloat volume of the contrasts would be zero as well. Mmh, maybe that is because I did not specify a -taumax. Just started a test run with -taumax 20, and each Slice N, NN. -- line is followed by a NBrainVoxs = line, so user error on my part. Redid an analysis right now, and the end result with -taumax 20 has way less significant activation outside the brain proper. Thanks for the explanation. Ahoi Sebastian Sebastian Moeller wrote: Hi All, as the subject line reveals, I have a question regarding mkanalysis-sess.new (running centos4_x86_64 3.0.1 pub stable, on SuSE 9.3, not that it matters...). My question is, is there any heuristic how to chose the -taumax parameter, that can be used in combination with a brainmask? I am wondering as the example usage from the fsfast workflow specifies a brainmask, but does not set -taumax, is that a useful approach? One more question about the brainmask I have is, (at least without a specified taumax) I still see non-uniform values in the sig volume, while actually expecting close to nothing, but I guess I have not groked how the masking is supposed to work... I would be happy for any pointers about this issue. And while on the matter, is there a way to allow empty conditions, i.e. use a sparse condition numbering in the .para files (trading the check for missing conditions versus the possibility to use stable identifiers for loads of conditions used over different days). Ahoi Sebastian -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Repeated-measures in mris_glm
Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers between-subjects designs. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Repeated-measures in mris_glm
There are two ways to do it: 1. You can use DOSS, making each subject it's own class. Then create one Variable. For a given input, set the variable to either +1 or -1 depending upon whether it corresponds to the first or second time point. Then create a contrast as [0 0 0 0 ... 0 0 0 1], where there are as many 0s as subjects. The last 1 will correspond to the Time Point variable. 2. Alternatively, if you are using mris_preproc, you can specify --paired-diff, then just use a one-sample group mean test. See the --help. This may be easier, and will also allow you to add a between subject factor. doug Fornito, Alexander wrote: Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers between-subjects designs. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Repeated-measures in mris_glm
Hi Doug, Is mri_preproc a new addition to the stable version? I'm using recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. I tried running the analysis through mris_glm as per option 1 as you described, but came across a problem. Command, error, and my FSGD are below. Thanks, Alex Command: mris_glm --surfmeas thickness --hemi lh --trgsubj ../average --fsgd ./test_fsgd.txt doss --beta ./beta_doss_thickness-100_lh bfloat --var ./var_doss_thickness-100_lh.w paint --y ./y_doss_thickness-100_lh_000.bfloat --nsmooth 100 gdfReadHeader: reading ./test_fsgd.txt INFO: ignoring tag 1 INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) = ncols (11) My FSGD: GroupDescriptorFile 1 Title Time 1 vs Time 2 Class class_time1_subj1 Class class_time1_subj2 Class class_time1_subj3 Class class_time1_subj4 Class class_time1_subj5 Class class_time2_subj1 Class class_time2_subj2 Class class_time2_subj3 Class class_time2_subj4 Class class_time2_subj5 Variables Time Input time1_subj1 class_time1_subj1 -1 Input time1_subj2 class_time1_subj2 -1 Input time1_subj3 class_time1_subj3 -1 Input time1_subj4 class_time1_subj4 -1 Input time1_subj5 class_time1_subj5 -1 Input time2_subj1 class_time2_subj1 1 Input time2_subj2 class_time2_subj2 1 Input time2_subj3 class_time2_subj3 1 Input time2_subj4 class_time2_subj4 1 Input time2_subj5 class_time2_subj5 1 DefaultVariable Time Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 9:31 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm There are two ways to do it: 1. You can use DOSS, making each subject it's own class. Then create one Variable. For a given input, set the variable to either +1 or -1 depending upon whether it corresponds to the first or second time point. Then create a contrast as [0 0 0 0 ... 0 0 0 1], where there are as many 0s as subjects. The last 1 will correspond to the Time Point variable. 2. Alternatively, if you are using mris_preproc, you can specify --paired-diff, then just use a one-sample group mean test. See the --help. This may be easier, and will also allow you to add a between subject factor. doug Fornito, Alexander wrote: Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers between-subjects designs. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Repeated-measures in mris_glm
Yes, mris_preproc is new with stable. In your FSGD file, try specifying the title as a single string without spaces. doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: Hi Doug, Is mri_preproc a new addition to the stable version? I'm using recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. I tried running the analysis through mris_glm as per option 1 as you described, but came across a problem. Command, error, and my FSGD are below. Thanks, Alex Command: mris_glm --surfmeas thickness --hemi lh --trgsubj ../average --fsgd ./test_fsgd.txt doss --beta ./beta_doss_thickness-100_lh bfloat --var ./var_doss_thickness-100_lh.w paint --y ./y_doss_thickness-100_lh_000.bfloat --nsmooth 100 gdfReadHeader: reading ./test_fsgd.txt INFO: ignoring tag 1 INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) = ncols (11) My FSGD: GroupDescriptorFile 1 Title Time 1 vs Time 2 Class class_time1_subj1 Class class_time1_subj2 Class class_time1_subj3 Class class_time1_subj4 Class class_time1_subj5 Class class_time2_subj1 Class class_time2_subj2 Class class_time2_subj3 Class class_time2_subj4 Class class_time2_subj5 Variables Time Input time1_subj1 class_time1_subj1 -1 Input time1_subj2 class_time1_subj2 -1 Input time1_subj3 class_time1_subj3 -1 Input time1_subj4 class_time1_subj4 -1 Input time1_subj5 class_time1_subj5 -1 Input time2_subj1 class_time2_subj1 1 Input time2_subj2 class_time2_subj2 1 Input time2_subj3 class_time2_subj3 1 Input time2_subj4 class_time2_subj4 1 Input time2_subj5 class_time2_subj5 1 DefaultVariable Time Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 9:31 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm There are two ways to do it: 1. You can use DOSS, making each subject it's own class. Then create one Variable. For a given input, set the variable to either +1 or -1 depending upon whether it corresponds to the first or second time point. Then create a contrast as [0 0 0 0 ... 0 0 0 1], where there are as many 0s as subjects. The last 1 will correspond to the Time Point variable. 2. Alternatively, if you are using mris_preproc, you can specify --paired-diff, then just use a one-sample group mean test. See the --help. This may be easier, and will also allow you to add a between subject factor. doug Fornito, Alexander wrote: Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers between-subjects designs. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Curvature
How should one interpret the curvature function...what is the essence of it's being...what does it mean? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Repeated-measures in mris_glm
I still get the same error message. Maybe I've coded the variable wrong? gdfReadHeader: reading ./test_fsgd.txt INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) = ncols (11) Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 11:43 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Repeated-measures in mris_glm Yes, mris_preproc is new with stable. In your FSGD file, try specifying the title as a single string without spaces. doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: Hi Doug, Is mri_preproc a new addition to the stable version? I'm using recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. I tried running the analysis through mris_glm as per option 1 as you described, but came across a problem. Command, error, and my FSGD are below. Thanks, Alex Command: mris_glm --surfmeas thickness --hemi lh --trgsubj ../average --fsgd ./test_fsgd.txt doss --beta ./beta_doss_thickness-100_lh bfloat --var ./var_doss_thickness-100_lh.w paint --y ./y_doss_thickness-100_lh_000.bfloat --nsmooth 100 gdfReadHeader: reading ./test_fsgd.txt INFO: ignoring tag 1 INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) = ncols (11) My FSGD: GroupDescriptorFile 1 Title Time 1 vs Time 2 Class class_time1_subj1 Class class_time1_subj2 Class class_time1_subj3 Class class_time1_subj4 Class class_time1_subj5 Class class_time2_subj1 Class class_time2_subj2 Class class_time2_subj3 Class class_time2_subj4 Class class_time2_subj5 Variables Time Input time1_subj1 class_time1_subj1 -1 Input time1_subj2 class_time1_subj2 -1 Input time1_subj3 class_time1_subj3 -1 Input time1_subj4 class_time1_subj4 -1 Input time1_subj5 class_time1_subj5 -1 Input time2_subj1 class_time2_subj11 Input time2_subj2 class_time2_subj21 Input time2_subj3 class_time2_subj31 Input time2_subj4 class_time2_subj41 Input time2_subj5 class_time2_subj51 DefaultVariable Time Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 9:31 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm There are two ways to do it: 1. You can use DOSS, making each subject it's own class. Then create one Variable. For a given input, set the variable to either +1 or -1 depending upon whether it corresponds to the first or second time point. Then create a contrast as [0 0 0 0 ... 0 0 0 1], where there are as many 0s as subjects. The last 1 will correspond to the Time Point variable. 2. Alternatively, if you are using mris_preproc, you can specify --paired-diff, then just use a one-sample group mean test. See the --help. This may be easier, and will also allow you to add a between subject factor. doug Fornito, Alexander wrote: Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers between-subjects designs. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Repeated-measures in mris_glm
Oh, I'm sorry. I see the problem now. When I said to create a class for each subject, I meant for each person, not for each FreeSurfer subject. So there should only be 5 classes, not 10. So do something like this: Class class_subj1 Class class_subj2 Class class_subj3 Class class_subj4 Class class_subj5 Variables Time Input time1_subj1 class_subj1 -1 Input time2_subj1 class_subj1 +1 ... doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: I still get the same error message. Maybe I've coded the variable wrong? gdfReadHeader: reading ./test_fsgd.txt INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) = ncols (11) Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 11:43 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Repeated-measures in mris_glm Yes, mris_preproc is new with stable. In your FSGD file, try specifying the title as a single string without spaces. doug On Tue, 11 Apr 2006, Fornito, Alexander wrote: Hi Doug, Is mri_preproc a new addition to the stable version? I'm using recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. I tried running the analysis through mris_glm as per option 1 as you described, but came across a problem. Command, error, and my FSGD are below. Thanks, Alex Command: mris_glm --surfmeas thickness --hemi lh --trgsubj ../average --fsgd ./test_fsgd.txt doss --beta ./beta_doss_thickness-100_lh bfloat --var ./var_doss_thickness-100_lh.w paint --y ./y_doss_thickness-100_lh_000.bfloat --nsmooth 100 gdfReadHeader: reading ./test_fsgd.txt INFO: ignoring tag 1 INFO: gd2mtx_method is doss ERROR: Design Matrix: nrows (10) = ncols (11) My FSGD: GroupDescriptorFile 1 Title Time 1 vs Time 2 Class class_time1_subj1 Class class_time1_subj2 Class class_time1_subj3 Class class_time1_subj4 Class class_time1_subj5 Class class_time2_subj1 Class class_time2_subj2 Class class_time2_subj3 Class class_time2_subj4 Class class_time2_subj5 Variables Time Input time1_subj1 class_time1_subj1 -1 Input time1_subj2 class_time1_subj2 -1 Input time1_subj3 class_time1_subj3 -1 Input time1_subj4 class_time1_subj4 -1 Input time1_subj5 class_time1_subj5 -1 Input time2_subj1 class_time2_subj1 1 Input time2_subj2 class_time2_subj2 1 Input time2_subj3 class_time2_subj3 1 Input time2_subj4 class_time2_subj4 1 Input time2_subj5 class_time2_subj5 1 DefaultVariable Time Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Tue 4/11/2006 9:31 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm There are two ways to do it: 1. You can use DOSS, making each subject it's own class. Then create one Variable. For a given input, set the variable to either +1 or -1 depending upon whether it corresponds to the first or second time point. Then create a contrast as [0 0 0 0 ... 0 0 0 1], where there are as many 0s as subjects. The last 1 will correspond to the Time Point variable. 2. Alternatively, if you are using mris_preproc, you can specify --paired-diff, then just use a one-sample group mean test. See the --help. This may be easier, and will also allow you to add a between subject factor. doug Fornito, Alexander wrote: Hi, I'd like to run a simple repeated-measures analysis tetsing for change in thickness measures between 2 time points. There is no between-subjects factor, only the effect of time. Do I just set up a standard DOSS FSGD file, or do I use a different format? The tutorial only covers between-subjects designs. Thanks, Alex Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph:+61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you,
