[Freesurfer] freesurfer ROIs for network analysis

t file to correspond with the label volumes? I'm looking for a simplified x,y,z coordinate file for about the 68 structures, rather than the grayordinates with every vertex. Finally, would the label names file be generated with both left and right hemispheres in the one file? Kind Regards, Stef

[Freesurfer] bbregister error

Hi Freesurfer users, I'm trying to run the bbregister command on the brain.mgz file. Here is the command line and resulting error: [12239012@psych2 ~/001ER]$ bbregister --s 001ER --mov mri/brain.mgz --reg register.dat ERROR: cannot find 001ER in /usr/local/apps/freesurfer/5.1.0/subjects I need

Re: [Freesurfer] Freesurfer Digest, Vol 135, Issue 28

JECTS_DIR environment variable is probably set > incorrectly. > > Does /usr/local/apps/freesurfer/5.1.0/subject/001ER exist? What is > SUBJECTS_DIR set to? > > SUBJECTS_DIR should be set to the directory containing "001ER". > > -Zeke > > On 05/19

[Freesurfer] orientation flipped after mri_label2vol

Hi Freesurfer, We've carried out the mri_label2vol step for ROIs in one hemisphere. When opening in ITKsnap the orientations appeared flipped, with the axial ROIs overlayed onto the coronal orientation, and coronal over the axial, and the sagittal plane appeared rotated. Can anyone help us fix thi