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
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