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All of the steps below are contained in the scripts file /Volumes/data9/surface/scripts/@prep_dir

To run this command type,

 /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

mkdir lastname_firstname

cd into directory

mkdir afni

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.

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