Namely, I was following the directions from the following:
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V
On Tue, Apr 19, 2011 at 12:33 PM, Allie Rosen rosen.allie@gmail.com wrote:
Hi Doug,
It worked with +1 -1 0. But I also have an agediff.mat file (0 0 +1 -1) that I'd like to look at. Therefore I'd be looking at age differences and also sex differences. Can I do this using DODS? I'm not sure if I'd be able to do that with 3 regressors.
So honestly I'm not even sure whether I should use DOSS or DODS. My groups are male and female and I'm not sure if there are differences between them. I thought that the first 2 regressors were male and female, and the 3rd and 4th were age. Am I correct?
Thanks, Allie
On Tue, Apr 19, 2011 at 12:26 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Hi Alli,e you are running it with DOSS which will create 4 regressors (MaleOffset, FemaleOff, AgeSlope). Your contrast has 4 columns. So change to DODS or change the number of column in your contrast. If you go with DODS, make sure to test for an interaction (ie, a contrast of 0 0 +1 -1). If you have substantial interaction, then testing the offsets is tricky. If you don't have an interaction, then change to DOSS and use (+1 -1 0).
doug
Allie Rosen wrote:
Update: ran on a different computer in the lab and progressed a little, but got the following error: "dimension mismatch between X and contrast sexdiff.mat X has 3 cols, C has 4 cols"
I am not positive what X is, but here is my FSGD file (abbreviated):
GroupDescriptorFile 1 Class Male Class Female Variables Age
Input C1 Female 27 Input C2 Female 53 Input C3 Male 22 Input C4 Female 62 Input C5 Male 27
And here is my contrast file:
1 -1 0 0
Any ideas?
Thank you, Allie
On Tue, Apr 19, 2011 at 11:51 AM, Allie Rosen <rosen.allie@gmail.commailto: rosen.allie@gmail.com> wrote:
Hi All,
I am running mri_glmfit and get the following error:
mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat gdfReadHeader: reading fsgd2.txt INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 37.9483 Class Means of each Continuous Variable 1 Male 34.5417 2 Female 40.3529 INFO: gd2mtx_method is doss Reading source surface /media/AMMONIS/fsSubjects/AR_normals/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470
$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /media/AMMONIS/fsSubjects/AR_normals cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat sysname Linux hostname Caduceus machine x86_64 user arosen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz logyflag 0 usedti 0 FSGD fsgd2.txt labelmask /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.insula.thickness.6.glmdir IllCondOK 0 DoFFx 0 Creating output directory lh.insula.thickness.6.glmdir Segmentation fault
The directory IS created, but contains only "mri_glmfit.log". Here are the contents:
$Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /media/AMMONIS/fsSubjects/AR_normals cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat sysname Linux hostname Caduceus machine x86_64 user arosen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz logyflag 0 usedti 0 FSGD fsgd2.txt labelmask /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.insula.thickness.6.glmdir IllCondOK 0 DoFFx 0
If this all sounds familiar, I realize that I've submitted this problem back in January and haven't managed to work it out. Any help would be appreciated!
Thank you, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto
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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
It depends on what you are looking for. If you are interested in the interaction (group-by-age), then you need DODS and [0 0 +1 -1]. If you are interested in differences in group offset/intercept, then you have some choices to make. If you are sure that there is no interaction, then simply use DOSS and [+1 -1 0]. If you suspect an interaction, then you need to test it as described above. If the above test comes out negative, then switch back to DOSS to test the difference between group offset.
doug
Allie Rosen wrote:
Namely, I was following the directions from the following:
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V
On Tue, Apr 19, 2011 at 12:33 PM, Allie Rosen <rosen.allie@gmail.com mailto:rosen.allie@gmail.com> wrote:
Hi Doug, It worked with +1 -1 0. But I also have an agediff.mat file (0 0 +1 -1) that I'd like to look at. Therefore I'd be looking at age differences and also sex differences. Can I do this using DODS? I'm not sure if I'd be able to do that with 3 regressors. So honestly I'm not even sure whether I should use DOSS or DODS. My groups are male and female and I'm not sure if there are differences between them. I thought that the first 2 regressors were male and female, and the 3rd and 4th were age. Am I correct? Thanks, Allie On Tue, Apr 19, 2011 at 12:26 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Alli,e you are running it with DOSS which will create 4 regressors (MaleOffset, FemaleOff, AgeSlope). Your contrast has 4 columns. So change to DODS or change the number of column in your contrast. If you go with DODS, make sure to test for an interaction (ie, a contrast of 0 0 +1 -1). If you have substantial interaction, then testing the offsets is tricky. If you don't have an interaction, then change to DOSS and use (+1 -1 0). doug Allie Rosen wrote: Update: ran on a different computer in the lab and progressed a little, but got the following error: "dimension mismatch between X and contrast sexdiff.mat X has 3 cols, C has 4 cols" I am not positive what X is, but here is my FSGD file (abbreviated): GroupDescriptorFile 1 Class Male Class Female Variables Age Input C1 Female 27 Input C2 Female 53 Input C3 Male 22 Input C4 Female 62 Input C5 Male 27 And here is my contrast file: 1 -1 0 0 Any ideas? Thank you, Allie On Tue, Apr 19, 2011 at 11:51 AM, Allie Rosen <rosen.allie@gmail.com <mailto:rosen.allie@gmail.com> <mailto:rosen.allie@gmail.com <mailto:rosen.allie@gmail.com>>> wrote: Hi All, I am running mri_glmfit and get the following error: mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat gdfReadHeader: reading fsgd2.txt INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 37.9483 Class Means of each Continuous Variable 1 Male 34.5417 2 Female 40.3529 INFO: gd2mtx_method is doss Reading source surface /media/AMMONIS/fsSubjects/AR_normals/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /media/AMMONIS/fsSubjects/AR_normals cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat sysname Linux hostname Caduceus machine x86_64 user arosen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz logyflag 0 usedti 0 FSGD fsgd2.txt labelmask /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.insula.thickness.6.glmdir IllCondOK 0 DoFFx 0 Creating output directory lh.insula.thickness.6.glmdir Segmentation fault The directory IS created, but contains only "mri_glmfit.log". Here are the contents: $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /media/AMMONIS/fsSubjects/AR_normals cmdline mri_glmfit --y lh.insula.thickness.6.mgz --fsgd fsgd2.txt doss --glmdir lh.insula.thickness.6.glmdir --surf fsaverage lh --C sexdiff.mat sysname Linux hostname Caduceus machine x86_64 user arosen FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /media/AMMONIS/fsSubjects/AR_normals/lh.insula.thickness.6.mgz logyflag 0 usedti 0 FSGD fsgd2.txt labelmask /media/AMMONIS/fsSubjects/AR_normals/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.insula.thickness.6.glmdir IllCondOK 0 DoFFx 0 If this all sounds familiar, I realize that I've submitted this problem back in January and haven't managed to work it out. Any help would be appreciated! Thank you, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Allie Rosen -
Douglas N Greve