yes, mean across space. for vertex wise, you'll probably have to go into matlab, something like

mask = MRIread('mask.mgh');

imask = find(mask.vol == 1);

cc = MRIread('concat.mgh');

ccmat = fast_vol2mat(cc);

cc_in_mask = ccmat(:,imask);

Hi Doug,

Thanks!

mri_segstats —i concat.mgh  --seg mask.mgh --avgwf data

1) concat.mgh is the stack of individual surfaces in fsaverage space

2) mask.mgh is the binarised mask from the sig.mgh 

3) --avgwf to produce the 2 columns of data (inside and outside)

The values from the --avgwf represent the mean value across the vertices in and outside the mask, yes? Can I get the vertex-wise data though? 

Appreciate it!

Best Wishes,

Elijah

On 31 July 2017 at 15:17:02, Douglas Greve (greve@nmr.mgh.harvard.edu) wrote:

You can use mri_segstats with either the --sum option (for an input with one time point) or --avgwf (for multiple). Pass your mask with --seg. By default it will give you both outside the mask (first column) and inside the mask (second column).

On 7/28/17 10:44 AM, Elijah Mak wrote:

Hi Freesurfer Team,

I have previously used mri_binarize to derive the mask.mgh from the sig.mgh after a first-level group comparison of cortical thickness. Now, I would like to extract the vertex data from from another modality surface within and outside the mask in individual subjects. Is there an nice workflow to do that?

Thanks a lot. I hope my question made sense!

Best Wishes,

Elijah 

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