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);
On 7/31/17 10:25 AM, Elijah Mak wrote:
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 ([email protected]
<mailto:[email protected]>) 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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