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
> <mailto:Freesurfer@nmr.mgh.harvard.edu>> <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
> >
> >
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
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Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422
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