Re: [Freesurfer] fsaverage label into functional space

This appears to be a bug in mri_label2vol when you specify a surface. Instead, you can create a volume in the conformed space, and then use mri_label2vol with that volume as the --seg input. BTW, you should use mri_label2label to map from fsaverage into the individual subject space, then do the two calls to mri_label2vol. doug

On 10/10/2019 1:02 PM, Lauri Tuominen wrote:

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Dear FreeSurfers!

I would like to confirm something before I proceed with my analyses. I think I am just confused again.

I am doing resting state analysis using fsfast. I am trying to use a label defined in the fsaverage space as a seed using the fcseed-config & fcseed-sess commands. Now these commands say that the label should be in fuctional space, which I gather is the space of the f.nii.

So in order to move the label into functional space I say:

mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label --o lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01 --hemi lh --temp ${projectdir}/${sessionj}/rest/001/f.nii --fill-ribbon --reg ${projectdir}/${session}/rest/register.dof6.lta

To my surprise, the voxel size here corresponds to the anatomical (orig.mgz) but not the functional space (f.nii). To test this further I did:

mri_label2vol --subject fsaverage --label lh.mylabel.in-fsaverage.label --o lh.mylabel.individualized.in-functional.mgz --proj frac 0 1 0.01 --hemi lh --temp $SUBJECTS_DIR/$/${sessionj}/mri/orig.mgz --fill-ribbon --reg ${projectdir}/${session}/rest/register.dof6.lta

And I get exactly the same ROI in the volume--p.

So just to confirm, is this what I want for the fcseed -commands?

Thank you so much again!

Lauri Tuominen

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