Beauchamp:PrepCortSurfModels: Difference between revisions
No edit summary |
|||
Line 5: | Line 5: | ||
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 | 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 | 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 | If only a single T1 was acquired, then an average dataset can be faked with the command | ||
Line 10: | Line 13: | ||
The instructions below assume that a dataset named ECanatavg+orig has already been created. | The instructions below assume that a dataset named ECanatavg+orig has already been created. | ||
== Automation == | == Automation == | ||
Revision as of 11:44, 21 May 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
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