Beauchamp:PrepCortSurfModels: Difference between revisions
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The scripts assumes that an anatomical named ECanatavg+orig exists in the current directory. | The scripts assumes that an anatomical named ECanatavg+orig exists in the current directory. | ||
e.g. | e.g. | ||
''' /Volumes/data9/surfaces/scripts/@prep_dir $ec $subj | |||
''' /Volumes/data9/surfaces/scripts/@prep_dir DB doe_jane | ''' /Volumes/data9/surfaces/scripts/@prep_dir DB doe_jane | ||
''' | ''' | ||
This will create surfaces in the directory doe_jane | This will create surfaces in the directory doe_jane |
Revision as of 11:53, 3 December 2008
Creating an Anatomical BRIK
Surfaces are created from an anatomical (T1) MRI dataset. Surface creation works best if two 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 ${ec}anatr1_1RegTo2+orig
or
3dAllineate -base {$ec}anatr2+orig -source {$ec}anatr2+orig -prefix ${ec}anatr1_1RegTo2 -verb -warp shift_rotate -cost mi -automask -1Dfile ${ec}anatr2toanatr1 3dmerge -gnzmean -nscale -prefix ${ec}anatavg {$ec}anatr2+orig ${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
NB: To access this script (or anything else on data9) then data9 must be mounted on your Mac. 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 $ec $subj
/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