TRACULA is a fiber tracking and white matter segmentation tool within FreeSurfer.
Fixes
The scripts rely on symbolic links, which cannot be created on Windows shared folders. To run in a VM with the SUBJECTS_DIR on the shared folder, the file "track-preproc" (trac-preproc as of 2013-08-20) has to be edited to change all the symbolic link creations to file-copy instead. This may cause a problem if the "linked" files are changed.
Running
Each subject needs T1 anatomicals that have been processing with the usual FreeSurfer analysis, and DTI data in the format of DICOM or custom nifti files. A configuration file is used to define subjects and locations.
The following commands are examples of running the preprocessing steps:
- tracl-all -c /mnt/hgfs/LinuxShare/tracula/dmrirc -prep
Configuration File (dmrirc)
This is a required file which is passed to the TRACULA processing steps. A reasonable place to save this is LinuxShare\tracula.
FreeSurfer Preprocessing
Make sure each subject has a successfully completed FreeSurfer preprocessing set of files.
DTI Data
Probably easiest to use an outside folder; if DICOM files are available, these will work (at least for Siemens scanners). Otherwise, the format is akin to FSL.
- Note that for Linux, spaces are a problem, so the file names must have spaces removed.