External Email - Use Caution
To confirm, your label is starting on the fsaverage surface. You can open
tksurfer fsaverage ?h pial and open the label and it shows up?
From my experience using fcseed-sess & fcseed-config using FS v6.0.0 what
you want to do is move the label from fsaverage -> subject native surface
-> subject native T1 volume and it will take care of the rest
So you would run:
label=your_label (without the .label at the end)
subject=your_new_subject
hemi=lh (or rh)
mri_label2label --srclabel $SUBJECTS_DIR/fsaverage/label/$label.label
--trglabel $SUBJECTS_DIR/$subject/label/$label.label --trgsubject $subject
--srcsubject fsaverage --hemi $hemi --srchemi $hemi --trghemi $hemi
--regmethod surface
mri_label2vol --label $SUBJECTS_DIR/$subject/label/$label.label --temp
$SUBEJCTS_DIR/$subject/mri/brainmask.mgz --fill-ribbon --subject $subject
--hemi $hemi --regheader $SUBJECTS_DIR/$subject/mri/brainmask.mgz --o
$SUBJECTS_DIR/$subject/mri/$label.mgz
The new file is what you would input as the "-seg $label.mgz" in the
fcseed-config command
On a related note -- in my tests of -proj-frac vs. -fill-ribbon == if you
want the full ROI from edge of the white surface to the pial surface you
should use -fill-ribbon -- see attached screenshot
[image: projfrac_vs_fill-ribbon.png]
On Thu, Oct 10, 2019 at 12:03 PM Lauri Tuominen <ljt...@utu.fi> wrote:
> External Email - Use Caution
>
> 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.
>
> So just to confirm, is this what I want for the fcseed -commands?
>
> Thank you so much again!
>
> Lauri Tuominen
>
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