Beauchamp:PrepCortSurfModels: Difference between revisions
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== 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 == | == Automation == | ||
Revision as of 12:39, 29 April 2008
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