Beauchamp:PrepCortSurfModels

Creating an Anatomical BRIK

Surfaces are created from an anatomical (T1) MRI dataset. Surface creation works best if 2 or more T1 datasets are acquired and averaged. This can be accomplished with the following commands. Motion correction is applied before averaging in case the subject moved between anatomies.

3dAllineate -base 3DSAG_T1_2.nii -source 3DSAG_T1_1.nii -prefix ${ec}anatr1_1RegTo2 -verb -warp shift_rotate -cost mi -automask -1Dfile ${ec}anatr2toanatr1
3dmerge -gnzmean -nscale -prefix ${ec}anatavg 3DSAG_T1_2.nii  ${ec}anatr1_1RegTo2+orig

If only a single T1 was acquired, then an average dataset can be faked with the command

 3dcopy 3DSAG_T1.nii ${ec}anatavg

The instructions below assume that a dataset named ECanatavg+orig has already been created.

Automation

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 a subject's anatomy (in AFNI format) is stored in a file name ECanatavg. e.g.

 cd /Volumes/data1/UT/DB/afni

Then, 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 ECanatavg+orig exists in the current directory. e.g.

 /Volumes/data9/surfaces/scripts/@prep_dir DB doe_jane

This will create surfaces in the directory doe_jane

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

ie.

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.

or

 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