All of the steps below are contained in the scripts file /Volumes/data9/surface/scripts/@prep_dir
To run this command first change into the directory where the subject's anatomy (in AFNI format) is stored.
/Volumes/data9/surfaces/scripts/@prep_dir ec subjname
Where ec is the two-letter experiment code and subjname is the subject's name in the format lastname_firstname. The scripts assumes that an anatomical named ec_anatavg+orig exists in the subject's AFNI directory, which must be in the standard location /Volumes/data1/UT/XX/afni (see creating AFNI BRIKs page)
/Volumes/data9/surfaces/scripts/@prep_dir BD doe_jane
If you don't have an ec_anatavg+orig anatomy, or the AFNI directory is in a different location, you can also run the script in the AFNI directory and specify the anatomy as a third argument (it must be in the current directory when the script is run.)
/Volumes/data9/surfaces/scripts/@prep_dir CJ CJ_120907 CJ_120907.anat+orig.BRIK
Initial setup in /surfaces
Make subject directory in /Volumes/data9/surfaces
cd into directory
copy high resolution scans into afni directory
3dcopy /Volumes/data1/UT/CG/afni/CGanatr1+orig ./CGanatr1
Creating FreeSurfer Directory Structures for Individual Subjects
FreeSurfer requires a specific directory structure for each subject. In addition FreeSurfer requires that subjects’ directories be listed in the $SUBJECTS_DIR. Since this is an environment variable, it can be set at anytime:
set SUBJECTS_DIR = /surfaces/subject_name/
The program mksubjdirs constructs the directory structure automatically.
cd $SUBJECTS_DIR mksubjdirs subjID
Importing AFNI Files into FreeSurfer
The mri_convert program is used to convert the BRIK/HEAD files into the mgz format (gzipped MGH file),:
mri_convert $SUBJECTS_DIR/afni/subjIDanatr+orig.BRIK $SUBJECTS_DIR/subjID/mri/001.mgz
This should be repeated for every anatomical scan with the number scheme 001.mgz, 002.mgz, 003.mgz, etc.
mri_convert afni/CAavganat+orig.BRIK CA/mri/001.mgz
if the averaging is done in AFNI (recommended method).
Ignore warnings issued by Freesurfer about using only one anatomical scan