Thank you for your response. I have 2 questions.

1. I want to extract a binary ROI after group analysis with the command:

mri_binarize --i lh.sig.nii.gz --min 9.13 --mask lh.V3A.nii.gz --o lh.ROI.nii.gz

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.ROI.nii.gz

When I overlayed lh.sig.V3A.nii.gz with freeview, I found the edge of the ROI are decimals and voxel inside the mask is 1. I also tried “mri_binarize --zero-edge” but it didn’t work.

My question is : how to make a binary ROI (all the voxels below 9.13 is zero). The output file is attached in the email.

2. I try to convert the binary ROI in fsaverage space into individual space and extract the average HRF contrast in the ROI in each subject. Here’s my command.

# resample the ces.nii.gz volume into the individual’s space

mri_vol2vol --mov subj1/ces.nii.gz --reg register.lta --fstarg --interp nearest --o subj1/lh.ces.anat.bb.mgh

# resample the ROI volume into the individual’s space

mri_surf2surf --hemi lh --srcsubject fsaverage --trgsubject subj1 --reg subj1/register.lta --sval stats/lh.ROI.nii.gz --tval stats/lh.ROI.anat.bb.mgz --hemi lh

# extract the average HRF contrast in the ROI from each subject

mri_segstats --i lh.ces.anat.bb.mgh --sum ces.masked.bb.stats --mask lh.sig.V3A.anat.bb.mgz
This step goes wrong with caution “ERROR: must specify a segmentation volume”

My question is : how to extract the average HRF contrast in the ROI from each subject ? Is there some option like "--m cespct” in funcroi-table-sess to extract average signal change?

Thanks

Star Xi

On 02/14/2020 23:14，Douglas N. Greve<dgreve@mgh.harvard.edu> wrote：

Is the hV5+MT label already a binary volume in the FS conformed 1mm space (ie, same space as orig.mgz)? And what do you mean by "constrained"?

On 2/13/2020 11:04 AM, Star Xi wrote:
External Email - Use Caution

FS experts,

Commonly, I can use mri_vol2vol -> mri_segstats to extract anatomical ROI from aparc or aseg template.

However, now I want to extract the average percent signal change in the hV5+/MT by constrained positive functional activation. The anatomical label is from other template.

My question is, after using mri_vol2vol, which command can extract signals from a given label with constrained activation ?

Thanks,

Star
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