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
wrote:
> then you need to add --surface fsaverage lh
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
> mailto:gr...@nmr.mgh.harvard.edu>> wr
It's surface-based analysis.
On Fri, Jul 22, 2016 at 1:43 PM, Douglas N Greve
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 se
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 wi
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
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 10:3
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
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 -
