Difference between revisions of "Anatomy Pipeline"
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==AC-PC Aligned Nifti Image== | ==AC-PC Aligned Nifti Image== | ||
Data can come off the scanner with arbitrary header information and in parrec format. So for each subject we start by defining a coordinate frame where 0,0,0 is at the anterior commissure, the anterior and posterior commissure are in the same X and Z planes, and the mid-line is centered in the image. Bob Dougherty wrote a nice tool to help with this. See [https://github.com/vistalab/vistasoft/blob/master/mrAnatomy/VolumeUtilities/mrAnatAverageAcpcNifti.m mrAnatAverageAcpcNifti]. The subject's T1-weighted image should be ac-pc aligned, resliced (preserving its resolution), and saved in the subject's anatomy directory. | Data can come off the scanner with arbitrary header information and in parrec format. So for each subject we start by defining a coordinate frame where 0,0,0 is at the anterior commissure, the anterior and posterior commissure are in the same X and Z planes, and the mid-line is centered in the image. Bob Dougherty wrote a nice tool to help with this. See [https://github.com/vistalab/vistasoft/blob/master/mrAnatomy/VolumeUtilities/mrAnatAverageAcpcNifti.m mrAnatAverageAcpcNifti]. The subject's T1-weighted image should be ac-pc aligned, resliced (preserving its resolution), and saved in the subject's anatomy directory. | ||
| − | + | cd /home/projects/MRI/[subid] | |
| − | parrec2nii -c | + | parrec2nii -c --scaling=fp *.PAR |
| − | mrAnatAverageAcpcNifti | + | im = niftiRead('T1path') |
| + | mrAnatAverageAcpcNifti({'T1path'}, '/home/projects/anatomy/[subid]/t1_acpc.nii.gz', diag(im.qto_xyz)) | ||
==Freesurfer Segmentation== | ==Freesurfer Segmentation== | ||
Revision as of 20:58, 17 August 2015
We collect a high resolution T1-weighted image on every subject, and use this image to define the coordinate space for all subsequent analyses. This section describes the processing steps for a subject's T1-weighted anatomy and should be performed before analyzing the rest of their MRI data.
AC-PC Aligned Nifti Image
Data can come off the scanner with arbitrary header information and in parrec format. So for each subject we start by defining a coordinate frame where 0,0,0 is at the anterior commissure, the anterior and posterior commissure are in the same X and Z planes, and the mid-line is centered in the image. Bob Dougherty wrote a nice tool to help with this. See mrAnatAverageAcpcNifti. The subject's T1-weighted image should be ac-pc aligned, resliced (preserving its resolution), and saved in the subject's anatomy directory.
cd /home/projects/MRI/[subid]
parrec2nii -c --scaling=fp *.PAR
im = niftiRead('T1path')
mrAnatAverageAcpcNifti({'T1path'}, '/home/projects/anatomy/[subid]/t1_acpc.nii.gz', diag(im.qto_xyz))
