TRACULA is a fiber tracking and white matter segmentation tool within FreeSurfer.

Running TRACULA

Required data

T1 with FreeSurfer processing

Each subject needs T1 anatomicals that have been processing with the usual FreeSurfer analysis. Typically, these are under the SUBJECTS_DIR LinuxShare\subjects4freesurfer. I'm not sure if the FreeSurfer processing needs to be successful (sometimes it fails).

DTI and bvecs/bvals

The DTI data need to be in the format of DICOM or custom nifti files. However, the DICOM files may be unreliable, as in practice, 64-direction Siemens DTI files with extra b0's caused errors. (It is possible this was because they were on the SUBJECTS_DIR on Windows network share.) The alternative is to use the FSL-ready DTI data in LinuxShare\subjects4fsl.

The bvals and bvecs files that TRACULA needs are slightly different to those used by FSL, so new files need to be created. The difference is that FSL has data across columns/volume, whereas TRACULA requires rows/volume, so they simply need to be flipped. Here is an example of how to do that.

Copy to local SUBJECTS_DIR

1) In Linux, check that you have a folder

/usr/local/freesurfer/subjects

If not, create it. This will also need the bert and fsaverage folders copied to it.

2) copy the T1 FreeSurfer subject to this folder. An example of a command (from a terminal in Linux):

...]$ cp -rv /mnt/hgfs/LinuxShare/subjects4freesurfer/CON302 /usr/local/freesurfer/subjects

Note the format of specifying the folder to copy, and the folder to copy into (as opposed to the destination folder); thus in the above example, the destination does not include "CON302".

3) Copy the DTI data to the same subjects folder:

Create the folder if it does not already exist:

...]$ mkdir /usr/local/freesurfer/subjects/CON302/DTI_b0corr

Copy the main data file:

...]$ cp /mnt/hgfs/LinuxShare/subjects4FSL/CON302/DTI_b0corr/data.ni* /usr/local/freesurfer/subjects/CON302/DTI_b0corr

Copy bvals4tracula.txt and bvecs4tracula.txt (see above to create them):

...]$ cp /mnt/hgfs/LinuxShare/subjects4FSL/CON302/DTI_b0corr/*4tracula.txt /usr/local/freesurfer/subjects/CON302/DTI_b0corr

Configuration File (dmrirc)

This is a required file which is passed to the TRACULA processing steps. Every new analysis requires a new or modified dmrirc file. If more than one person is analyzing the same datasest, best practice is to save each analysis as a unique file. A reasonable place to save files is LinuxShare\tracula.

Once you have a basic file, the most common change will be the subject name.

Example

Run TRACULA preprocessing

There are three commands to the preprocessing. Each command uses the dmrirc file, so in the samples below, you would change the "-c" parameter to the file you created.

trac-all -prep -c /mnt/hgfs/LinuxShare/tracula/dmrirc_VM.txt

trac-all -bedp -c /mnt/hgfs/LinuxShare/tracula/dmrirc_VM.txt

trac-all -path -c /mnt/hgfs/LinuxShare/tracula/dmrirc_VM.txt

These can be combined into one command, to run all three steps at once, by separating with "&&". (Separating with ";" semicolons will run all three commands indepedently, whereas "&&" will stop if the first command fails, which is what we want.) Thus the most command command will be:

...]$ trac-all -prep -c /mnt/hgfs/LinuxShare/tracula/dmrirc_VM.txt && trac-all -bedp -c /mnt/hgfs/LinuxShare/tracula/dmrirc_VM.txt && trac-all -path -c /mnt/hgfs/LinuxShare/tracula/dmrirc_VM.txt

Viewing Paths

The TRACULA portion of the wiki has several examples of the commands you will need to type. You need to adjust the location of the files.

Example to view single track:

...]$ freeview -v /usr/local/freesurfer/subjects/CON302/dmri/dtifit_FA.nii.gz /usr/local/freesurfer/subjects/CON302/dpath/lh.ilf_AS_avg33_mni_bbr/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red'

Example to view all tracks:

...]$ freeview -v /usr/local/freesurfer/subjects/CON302/dmri/dtifit_FA.nii.gz -tv /usr/local/freesurfer/subjects/CON302/dpath/merged_avg33_mni_bbr.mgz

Saving Outputs

You will want to copy the results back to the LinuxShare. All TRACULA outputs are in the subject "dmri" and "dpath" subfolders:

...]$ cp -rv /usr/local/freesurfer/subjects/CON302/dmri* /mnt/hgfs/LinuxShare/subjects4freesurfer/CON302

...]$ cp -rv /usr/local/freesurfer/subjects/CON302/dpath /mnt/hgfs/LinuxShare/subjects4freesurfer/CON302

The results will be available to everyone. Viewing paths and measure stats will require adjusting the file location.

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.

Technical Note: Issues running in a VM*

The scripts rely on symbolic links, which cannot be created on Windows shared folders. Thus, the SUBJECTS_DIR must be local, and under the usual VM setup we use, the files need to be copied locally, and the local SUBJECTS_DIR set.

An alternative that does not work is to run with the SUBJECTS_DIR on the shared folder. I did test by editing the file "track-preproc" (trac-preproc as of 2013-08-20) to change all the symbolic link creations to file-copy instead. Although the initial preprocessing step worked with this edited file, it crashed later on. Even had this worked, it may cause a problem if the "linked" files are changed.

*VM = Virtual Machine

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