It sounds like you want to convert your label into a binary mask to use with mri_fdr. Use mri_label2label, something like

mri_label2label --srclabel your.label --s subject --hemi lh --outmask your.label.nii.gz

Run with --help to get more info

On 03/14/2018 10:41 PM, Chen Jen-I. wrote:

This is surface-based analysis. I used tksurfer to load the mask.mgh as overlay e.g. tksurfer fsaverage rh inflated -fthresh 2.3 -overlay mask.mgh -delink -curv -gray

The mask.mgh file is from the GLMFIT folder after I ran mri_glmfit on my cortical thickness data within the areas set by the label that I have specified

Thanks.

Jeni Chen

Douglas N. Grevehttps://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N.+Greve%22 Wed, 14 Mar 2018 15:32:51 -0700https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20180314

Is this a volume or surface-based analysis? How did you try to visualize it?

On Mar 10, 2018, at 12:56 AM, Chen Jen-I. <jen-i.chen@umontreal.camailto:jen-i.chen@umontreal.ca> wrote:

Hello,

I want to do a FDR correction using mri_fdr within a ROI mask (in .label format). I see the option of passing the sig.mgh volume through a mask, and I read that one can use the mask.mgh in the GLMFIT folder. What is this mask.mgh? I tried to visualize it in Freeview but it doesn’t look like a mask but rather some sort of geometric form. If I have labels as my ROI, how do I convert that into a .mgh format to be used in mri_fdr? (I tried simply using the label file first and obviously that didn’t work…)

Thank you in advance,

Jeni Chen