Dear FreeSurfer experts,
I would like to get labels, get them in MNI305 space and to
visualize them on the brain.mgz, which to be in MNI305.
I used following:
a) To get labels in MNI
$FREESURFER_HOME/bin/make_average_subject --out asub1
--subjects sub1
#creat labels
mkdir $SUBJECTS_DIR/sub1/labels
$FREESURFER_HOME/bin/mri_annotation2label --subject sub1 --hemi lh --outdir
#transform label to MNI305
$FREESURFER_HOME/bin/mri_label2label --srcsubject sub1 --srclabel
$SUBJECTS_DIR/sub1/labels/lh.precentral.label --trgsubject asub1 --trglabel
$SUBJECTS_DIR/sub1/labels/lh.precentral_mni305.label --regmethod surface
--hemi lh
b) To visualize
tkregister2 --mov
$SUBJECTS_DIR/asub1/mri/brain.mgz --noedit --s asub1 --regheader --reg
$SUBJECTS_DIR/asub1/mri/register.dat
$FREESURFER_HOME/bin/mri_label2vol
--label ./lh.postcentral_mni305.label --temp $SUBJECTS_DIR/asub1/mri/brain.mgz
--subject asub1 --hemi lh --o asub1_lh_postcentral305.nii.gz --reg
$SUBJECTS_DIR/asub1/mri/register.dat
$FREESURFER_HOME/bin/mri_convert
$SUBJECTS_DIR/asub1/mri/brain.mgz $SUBJECTS_DIR/asub1/mri/abrain305.nii.gz
Is this correct?
Thank you.
Peka
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