Hello freesurfers,
I would like to use mri_glmfit with --mask but I get this error: dimension mismatch 1 between y and mask. I created a binary mask from 22 aparc labels (using mri_binarize) and I would like to run a surface-based analysis only on those regions. The command I use is:
mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz --glmdir lh.group_diff_g2v0.glmdir
The input file was generated with this command: mris_preproc --fsgd g2v0.fsgd --cache-in thickness.fwhm15.fsaverage --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh
From the error, it seems that I am not using the right input file. What
kind of input file should be used with a mask?
I also thought to use --label but I am not sure how to combine my 22 labels in one single label. mris_label2annot can combine them but the output is an annotation file not a label.
As a note, we will want to do FDR correction, not MC.
Thanks! Mihaela
How did you create the mask? It should be a surface overlay in fsaverage space, ie, you should be able to view it with
tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1
On 07/21/2016 01:51 PM, Mihaela Stefan wrote:
Hello freesurfers,
I would like to use mri_glmfit with --mask but I get this error: dimension mismatch 1 between y and mask. I created a binary mask from 22 aparc labels (using mri_binarize) and I would like to run a surface-based analysis only on those regions. The command I use is:
mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz --glmdir lh.group_diff_g2v0.glmdir
The input file was generated with this command: mris_preproc --fsgd g2v0.fsgd --cache-in thickness.fwhm15.fsaverage --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh
From the error, it seems that I am not using the right input file. What kind of input file should be used with a mask?
I also thought to use --label but I am not sure how to combine my 22 labels in one single label. mris_label2annot can combine them but the output is an annotation file not a label.
As a note, we will want to do FDR correction, not MC.
Thanks! Mihaela
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
I used this command: mri_binarize --match 1035 1028 1003 1027 1031 1008 1002 1026 1018 1020 1019 --i aparc+aseg.mgz --o lh22mask.mgz
When I checked it first time, I opened it as a volume and it looked okay to me. Now I was able to view it in tksurfer but it looks weird. See attachment.
Alternatively, I was able to create a label with mri_mergelabels: mri_mergelabels -i rh.insula.label -i rh.superiorfrontal.label -i rh.caudalmiddlefrontal.label -i rh.rostralmiddlefrontal.label -i rh.supramarginal.label -i rh.inferiorparietal.label -i rh.caudalanteriorcingulate.label -i rh.rostralanteriorcingulate.label -i rh.parsopercularis.label -i rh.parstriangularis.label -i rh.parsorbitalis.label -o rh.22mask.label
The mri_glmfit command seemed to have run successfully. However, the results from the ROI analysis are almost identical with the whole brain analysis. I find that surprising. Does it make sense statistically?
Here is the command I used for the whole brain analysis: mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.group_diff_g2v0WB.glmdir
And the command with the label for the ROI analysis: mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir lh.group_diff_g2v0.glmdir
Thanks! Mihaela
On Thu, Jul 21, 2016 at 5:55 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
How did you create the mask? It should be a surface overlay in fsaverage space, ie, you should be able to view it with
tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1
On 07/21/2016 01:51 PM, Mihaela Stefan wrote:
Hello freesurfers,
I would like to use mri_glmfit with --mask but I get this error: dimension mismatch 1 between y and mask. I created a binary mask from 22 aparc labels (using mri_binarize) and I would like to run a surface-based analysis only on those regions. The command I use is:
mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz --glmdir lh.group_diff_g2v0.glmdir
The input file was generated with this command: mris_preproc --fsgd g2v0.fsgd --cache-in thickness.fwhm15.fsaverage --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh
From the error, it seems that I am not using the right input file. What kind of input file should be used with a mask?
I also thought to use --label but I am not sure how to combine my 22 labels in one single label. mris_label2annot can combine them but the output is an annotation file not a label.
As a note, we will want to do FDR correction, not MC.
Thanks! Mihaela
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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
What was your visualization command? You should probably run mri_vol2surf with --projfract 0.5 and --interp nearest to get a surface map. But it begs the question as to why you would do binarize the aparc+aseg to get surface ROIs (you should just use the ?h.aparc.annot). doug
On 07/22/2016 10:38 AM, Mihaela Stefan wrote:
Hi Doug,
I used this command: mri_binarize --match 1035 1028 1003 1027 1031 1008 1002 1026 1018 1020 1019 --i aparc+aseg.mgz --o lh22mask.mgz
When I checked it first time, I opened it as a volume and it looked okay to me. Now I was able to view it in tksurfer but it looks weird. See attachment.
Alternatively, I was able to create a label with mri_mergelabels: mri_mergelabels -i rh.insula.label -i rh.superiorfrontal.label -i rh.caudalmiddlefrontal.label -i rh.rostralmiddlefrontal.label -i rh.supramarginal.label -i rh.inferiorparietal.label -i rh.caudalanteriorcingulate.label -i rh.rostralanteriorcingulate.label -i rh.parsopercularis.label -i rh.parstriangularis.label -i rh.parsorbitalis.label -o rh.22mask.label
The mri_glmfit command seemed to have run successfully. However, the results from the ROI analysis are almost identical with the whole brain analysis. I find that surprising. Does it make sense statistically?
Here is the command I used for the whole brain analysis: mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.group_diff_g2v0WB.glmdir
And the command with the label for the ROI analysis: mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir lh.group_diff_g2v0.glmdir
Thanks! Mihaela
On Thu, Jul 21, 2016 at 5:55 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
How did you create the mask? It should be a surface overlay in fsaverage space, ie, you should be able to view it with tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1 On 07/21/2016 01:51 PM, Mihaela Stefan wrote: > Hello freesurfers, > > I would like to use mri_glmfit with --mask but I get this error: > dimension mismatch 1 between y and mask. > I created a binary mask from 22 aparc labels (using mri_binarize) and > I would like to run a surface-based analysis only on those regions. > The command I use is: > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz --glmdir > lh.group_diff_g2v0.glmdir > > The input file was generated with this command: > mris_preproc --fsgd g2v0.fsgd --cache-in thickness.fwhm15.fsaverage > --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh > > From the error, it seems that I am not using the right input file. > What kind of input file should be used with a mask? > > I also thought to use --label but I am not sure how to combine my 22 > labels in one single label. mris_label2annot can combine them but the > output is an annotation file not a label. > > As a note, we will want to do FDR correction, not MC. > > Thanks! > Mihaela > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I tried that, too and it seemed to work. I extracted the ROIs from ?h.aparc.annot and merged them into a single label with mri_mergelabels then I ran mri_glmfit. Now I am not sure I used the correct command to mask the search:
mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir lh.group_diff_g2v0.glmdir
So I used my own label instead of ?h.aparc.annot. Does the above command look right?
Thanks again! Mihaela
On Fri, Jul 22, 2016 at 12:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
What was your visualization command? You should probably run mri_vol2surf with --projfract 0.5 and --interp nearest to get a surface map. But it begs the question as to why you would do binarize the aparc+aseg to get surface ROIs (you should just use the ?h.aparc.annot). doug
On 07/22/2016 10:38 AM, Mihaela Stefan wrote:
Hi Doug,
I used this command: mri_binarize --match 1035 1028 1003 1027 1031 1008 1002 1026 1018 1020 1019 --i aparc+aseg.mgz --o lh22mask.mgz
When I checked it first time, I opened it as a volume and it looked okay to me. Now I was able to view it in tksurfer but it looks weird. See attachment.
Alternatively, I was able to create a label with mri_mergelabels: mri_mergelabels -i rh.insula.label -i rh.superiorfrontal.label -i rh.caudalmiddlefrontal.label -i rh.rostralmiddlefrontal.label -i rh.supramarginal.label -i rh.inferiorparietal.label -i rh.caudalanteriorcingulate.label -i rh.rostralanteriorcingulate.label -i rh.parsopercularis.label -i rh.parstriangularis.label -i rh.parsorbitalis.label -o rh.22mask.label
The mri_glmfit command seemed to have run successfully. However, the results from the ROI analysis are almost identical with the whole brain analysis. I find that surprising. Does it make sense statistically?
Here is the command I used for the whole brain analysis: mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex --glmdir lh.group_diff_g2v0WB.glmdir
And the command with the label for the ROI analysis: mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir lh.group_diff_g2v0.glmdir
Thanks! Mihaela
On Thu, Jul 21, 2016 at 5:55 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
How did you create the mask? It should be a surface overlay in fsaverage space, ie, you should be able to view it with tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1 On 07/21/2016 01:51 PM, Mihaela Stefan wrote: > Hello freesurfers, > > I would like to use mri_glmfit with --mask but I get this error: > dimension mismatch 1 between y and mask. > I created a binary mask from 22 aparc labels (using mri_binarize) and > I would like to run a surface-based analysis only on those regions. > The command I use is: > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz --glmdir > lh.group_diff_g2v0.glmdir > > The input file was generated with this command: > mris_preproc --fsgd g2v0.fsgd --cache-in thickness.fwhm15.fsaverage > --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh > > From the error, it seems that I am not using the right input file. > What kind of input file should be used with a mask? > > I also thought to use --label but I am not sure how to combine my22
> labels in one single label. mris_label2annot can combine them but the > output is an annotation file not a label. > > As a note, we will want to do FDR correction, not MC. > > Thanks! > Mihaela > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Are you doing volume or surface-based analysis? If volume, then you'll need a volume mask and the --label is not appropriate.
On 07/22/2016 01:36 PM, Mihaela Stefan wrote:
I tried that, too and it seemed to work. I extracted the ROIs from ?h.aparc.annot and merged them into a single label with mri_mergelabels then I ran mri_glmfit. Now I am not sure I used the correct command to mask the search:
mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir lh.group_diff_g2v0.glmdir
So I used my own label instead of ?h.aparc.annot. Does the above command look right?
Thanks again! Mihaela
On Fri, Jul 22, 2016 at 12:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What was your visualization command? You should probably run mri_vol2surf with --projfract 0.5 and --interp nearest to get a surface map. But it begs the question as to why you would do binarize the aparc+aseg to get surface ROIs (you should just use the ?h.aparc.annot). doug On 07/22/2016 10:38 AM, Mihaela Stefan wrote: > Hi Doug, > > I used this command: > mri_binarize --match 1035 1028 1003 1027 1031 1008 1002 1026 1018 1020 > 1019 --i aparc+aseg.mgz --o lh22mask.mgz > > When I checked it first time, I opened it as a volume and it looked > okay to me. > Now I was able to view it in tksurfer but it looks weird. See attachment. > > > Alternatively, I was able to create a label with mri_mergelabels: > mri_mergelabels -i rh.insula.label -i rh.superiorfrontal.label -i > rh.caudalmiddlefrontal.label -i rh.rostralmiddlefrontal.label -i > rh.supramarginal.label -i rh.inferiorparietal.label -i > rh.caudalanteriorcingulate.label -i rh.rostralanteriorcingulate.label > -i rh.parsopercularis.label -i rh.parstriangularis.label -i > rh.parsorbitalis.label -o rh.22mask.label > > The mri_glmfit command seemed to have run successfully. However, the > results from the ROI analysis are almost identical with the whole > brain analysis. I find that surprising. Does it make sense statistically? > > Here is the command I used for the whole brain analysis: > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > group.diff.mtx --surf fsaverage lh --cortex --glmdir > lh.group_diff_g2v0WB.glmdir > > And the command with the label for the ROI analysis: > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir > lh.group_diff_g2v0.glmdir > > Thanks! > Mihaela > > > On Thu, Jul 21, 2016 at 5:55 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > How did you create the mask? It should be a surface overlay in > fsaverage > space, ie, you should be able to view it with > > tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1 > > On 07/21/2016 01:51 PM, Mihaela Stefan wrote: > > Hello freesurfers, > > > > I would like to use mri_glmfit with --mask but I get this error: > > dimension mismatch 1 between y and mask. > > I created a binary mask from 22 aparc labels (using > mri_binarize) and > > I would like to run a surface-based analysis only on those regions. > > The command I use is: > > > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > > lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz --glmdir > > lh.group_diff_g2v0.glmdir > > > > The input file was generated with this command: > > mris_preproc --fsgd g2v0.fsgd --cache-in thickness.fwhm15.fsaverage > > --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh > > > > From the error, it seems that I am not using the right input file. > > What kind of input file should be used with a mask? > > > > I also thought to use --label but I am not sure how to combine my 22 > > labels in one single label. mris_label2annot can combine them > but the > > output is an annotation file not a label. > > > > As a note, we will want to do FDR correction, not MC. > > > > Thanks! > > Mihaela > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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It's surface-based analysis.
On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Are you doing volume or surface-based analysis? If volume, then you'll need a volume mask and the --label is not appropriate.
On 07/22/2016 01:36 PM, Mihaela Stefan wrote:
I tried that, too and it seemed to work. I extracted the ROIs from ?h.aparc.annot and merged them into a single label with mri_mergelabels then I ran mri_glmfit. Now I am not sure I used the correct command to mask the search:
mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir lh.group_diff_g2v0.glmdir
So I used my own label instead of ?h.aparc.annot. Does the above command look right?
Thanks again! Mihaela
On Fri, Jul 22, 2016 at 12:34 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What was your visualization command? You should probably run mri_vol2surf with --projfract 0.5 and --interp nearest to get a surface map. But it begs the question as to why you would do binarize the aparc+aseg to get surface ROIs (you should just use the ?h.aparc.annot). doug On 07/22/2016 10:38 AM, Mihaela Stefan wrote: > Hi Doug, > > I used this command: > mri_binarize --match 1035 1028 1003 1027 1031 1008 1002 1026 1018 1020 > 1019 --i aparc+aseg.mgz --o lh22mask.mgz > > When I checked it first time, I opened it as a volume and it looked > okay to me. > Now I was able to view it in tksurfer but it looks weird. See attachment. > > > Alternatively, I was able to create a label with mri_mergelabels: > mri_mergelabels -i rh.insula.label -i rh.superiorfrontal.label -i > rh.caudalmiddlefrontal.label -i rh.rostralmiddlefrontal.label -i > rh.supramarginal.label -i rh.inferiorparietal.label -i > rh.caudalanteriorcingulate.label -i rh.rostralanteriorcingulate.label > -i rh.parsopercularis.label -i rh.parstriangularis.label -i > rh.parsorbitalis.label -o rh.22mask.label > > The mri_glmfit command seemed to have run successfully. However,the
> results from the ROI analysis are almost identical with the whole > brain analysis. I find that surprising. Does it make sense statistically? > > Here is the command I used for the whole brain analysis: > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > group.diff.mtx --surf fsaverage lh --cortex --glmdir > lh.group_diff_g2v0WB.glmdir > > And the command with the label for the ROI analysis: > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir > lh.group_diff_g2v0.glmdir > > Thanks! > Mihaela > > > On Thu, Jul 21, 2016 at 5:55 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > How did you create the mask? It should be a surface overlay in > fsaverage > space, ie, you should be able to view it with > > tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1 > > On 07/21/2016 01:51 PM, Mihaela Stefan wrote: > > Hello freesurfers, > > > > I would like to use mri_glmfit with --mask but I get this error: > > dimension mismatch 1 between y and mask. > > I created a binary mask from 22 aparc labels (using > mri_binarize) and > > I would like to run a surface-based analysis only on those regions. > > The command I use is: > > > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > > lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz --glmdir > > lh.group_diff_g2v0.glmdir > > > > The input file was generated with this command: > > mris_preproc --fsgd g2v0.fsgd --cache-in thickness.fwhm15.fsaverage > > --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh > > > > From the error, it seems that I am not using the right input file. > > What kind of input file should be used with a mask? > > > > I also thought to use --label but I am not sure how to combine my 22 > > labels in one single label. mris_label2annot can combine them > but the > > output is an annotation file not a label. > > > > As a note, we will want to do FDR correction, not MC. > > > > Thanks! > > Mihaela > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
then you need to add --surface fsaverage lh to the mri_glmfit command line, otherwise it thinks it is a volume-based analysis
On 07/22/2016 01:58 PM, Mihaela Stefan wrote:
It's surface-based analysis.
On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Are you doing volume or surface-based analysis? If volume, then you'll need a volume mask and the --label is not appropriate. On 07/22/2016 01:36 PM, Mihaela Stefan wrote: > I tried that, too and it seemed to work. I extracted the ROIs from > ?h.aparc.annot and merged them into a single label with > mri_mergelabels then I ran mri_glmfit. Now I am not sure I used the > correct command to mask the search: > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir > lh.group_diff_g2v0.glmdir > > So I used my own label instead of ?h.aparc.annot. Does the above > command look right? > > Thanks again! > Mihaela > > On Fri, Jul 22, 2016 at 12:34 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > What was your visualization command? You should probably run > mri_vol2surf with --projfract 0.5 and --interp nearest to get a > surface > map. But it begs the question as to why you would do binarize the > aparc+aseg to get surface ROIs (you should just use the > ?h.aparc.annot). > doug > > On 07/22/2016 10:38 AM, Mihaela Stefan wrote: > > Hi Doug, > > > > I used this command: > > mri_binarize --match 1035 1028 1003 1027 1031 1008 1002 1026 > 1018 1020 > > 1019 --i aparc+aseg.mgz --o lh22mask.mgz > > > > When I checked it first time, I opened it as a volume and it looked > > okay to me. > > Now I was able to view it in tksurfer but it looks weird. See > attachment. > > > > > > Alternatively, I was able to create a label with mri_mergelabels: > > mri_mergelabels -i rh.insula.label -i rh.superiorfrontal.label -i > > rh.caudalmiddlefrontal.label -i rh.rostralmiddlefrontal.label -i > > rh.supramarginal.label -i rh.inferiorparietal.label -i > > rh.caudalanteriorcingulate.label -i > rh.rostralanteriorcingulate.label > > -i rh.parsopercularis.label -i rh.parstriangularis.label -i > > rh.parsorbitalis.label -o rh.22mask.label > > > > The mri_glmfit command seemed to have run successfully. However, the > > results from the ROI analysis are almost identical with the whole > > brain analysis. I find that surprising. Does it make sense > statistically? > > > > Here is the command I used for the whole brain analysis: > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > > group.diff.mtx --surf fsaverage lh --cortex --glmdir > > lh.group_diff_g2v0WB.glmdir > > > > And the command with the label for the ROI analysis: > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > > group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir > > lh.group_diff_g2v0.glmdir > > > > Thanks! > > Mihaela > > > > > > On Thu, Jul 21, 2016 at 5:55 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > How did you create the mask? It should be a surface overlay in > > fsaverage > > space, ie, you should be able to view it with > > > > tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1 > > > > On 07/21/2016 01:51 PM, Mihaela Stefan wrote: > > > Hello freesurfers, > > > > > > I would like to use mri_glmfit with --mask but I get this > error: > > > dimension mismatch 1 between y and mask. > > > I created a binary mask from 22 aparc labels (using > > mri_binarize) and > > > I would like to run a surface-based analysis only on those > regions. > > > The command I use is: > > > > > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd > dods --C > > > lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz > --glmdir > > > lh.group_diff_g2v0.glmdir > > > > > > The input file was generated with this command: > > > mris_preproc --fsgd g2v0.fsgd --cache-in > thickness.fwhm15.fsaverage > > > --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh > > > > > > From the error, it seems that I am not using the right > input file. > > > What kind of input file should be used with a mask? > > > > > > I also thought to use --label but I am not sure how to > combine my 22 > > > labels in one single label. mris_label2annot can combine them > > but the > > > output is an annotation file not a label. > > > > > > As a note, we will want to do FDR correction, not MC. > > > > > > Thanks! > > > Mihaela > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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 mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > 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 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I did that. The command I use is: mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir lh.group_diff_g2v0.glmdir
On Fri, Jul 22, 2016 at 2:09 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
then you need to add --surface fsaverage lh to the mri_glmfit command line, otherwise it thinks it is a volume-based analysis
On 07/22/2016 01:58 PM, Mihaela Stefan wrote:
It's surface-based analysis.
On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Are you doing volume or surface-based analysis? If volume, thenyou'll
need a volume mask and the --label is not appropriate. On 07/22/2016 01:36 PM, Mihaela Stefan wrote: > I tried that, too and it seemed to work. I extracted the ROIs from > ?h.aparc.annot and merged them into a single label with > mri_mergelabels then I ran mri_glmfit. Now I am not sure I used the > correct command to mask the search: > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir > lh.group_diff_g2v0.glmdir > > So I used my own label instead of ?h.aparc.annot. Does the above > command look right? > > Thanks again! > Mihaela > > On Fri, Jul 22, 2016 at 12:34 PM, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > What was your visualization command? You should probably run > mri_vol2surf with --projfract 0.5 and --interp nearest to get a > surface > map. But it begs the question as to why you would do binarize the > aparc+aseg to get surface ROIs (you should just use the > ?h.aparc.annot). > doug > > On 07/22/2016 10:38 AM, Mihaela Stefan wrote: > > Hi Doug, > > > > I used this command: > > mri_binarize --match 1035 1028 1003 1027 1031 1008 1002 1026 > 1018 1020 > > 1019 --i aparc+aseg.mgz --o lh22mask.mgz > > > > When I checked it first time, I opened it as a volume and it looked > > okay to me. > > Now I was able to view it in tksurfer but it looks weird. See > attachment. > > > > > > Alternatively, I was able to create a label with mri_mergelabels: > > mri_mergelabels -i rh.insula.label -i rh.superiorfrontal.label -i > > rh.caudalmiddlefrontal.label -i rh.rostralmiddlefrontal.label -i > > rh.supramarginal.label -i rh.inferiorparietal.label -i > > rh.caudalanteriorcingulate.label -i > rh.rostralanteriorcingulate.label > > -i rh.parsopercularis.label -i rh.parstriangularis.label -i > > rh.parsorbitalis.label -o rh.22mask.label > > > > The mri_glmfit command seemed to have run successfully. However, the > > results from the ROI analysis are almost identical with the whole > > brain analysis. I find that surprising. Does it make sense > statistically? > > > > Here is the command I used for the whole brain analysis: > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > > group.diff.mtx --surf fsaverage lh --cortex --glmdir > > lh.group_diff_g2v0WB.glmdir > > > > And the command with the label for the ROI analysis: > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgd g2v0.fsgd dods --C > > group.diff.mtx --surf fsaverage lh --label lh.22mask.label --glmdir > > lh.group_diff_g2v0.glmdir > > > > Thanks! > > Mihaela > > > > > > On Thu, Jul 21, 2016 at 5:55 PM, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > How did you create the mask? It should be a surface overlay in > > fsaverage > > space, ie, you should be able to view it with > > > > tksurfer fsaverage lh inflated -ov mask.mgz -fminmax .1 1 > > > > On 07/21/2016 01:51 PM, Mihaela Stefan wrote: > > > Hello freesurfers, > > > > > > I would like to use mri_glmfit with --mask but I get this > error: > > > dimension mismatch 1 between y and mask. > > > I created a binary mask from 22 aparc labels (using > > mri_binarize) and > > > I would like to run a surface-based analysis only on those > regions. > > > The command I use is: > > > > > > mri_glmfit --y lh.g2v0.thickness.15.mgh --fsgdg2v0.fsgd
> dods --C > > > lh.group.diff.mtx --surf fsaverage lh --mask lh22mask.mgz > --glmdir > > > lh.group_diff_g2v0.glmdir > > > > > > The input file was generated with this command: > > > mris_preproc --fsgd g2v0.fsgd --cache-in > thickness.fwhm15.fsaverage > > > --target fsaverage --hemi lh --out lh.g2v0.thickness.15.mgh > > > > > > From the error, it seems that I am not using the right > input file. > > > What kind of input file should be used with a mask? > > > > > > I also thought to use --label but I am not sure how to > combine my 22 > > > labels in one single label. mris_label2annot can combine them > > but the > > > output is an annotation file not a label. > > > > > > As a note, we will want to do FDR correction, not MC. > > > > > > Thanks! > > > Mihaela > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 tel:617-724-2358>
> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > >ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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 mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > 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 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Douglas N Greve -
Mihaela Stefan