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.
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