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
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