Page Comparison

...

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 this files is LinuxShare\tracula.

...

A configuration file is used to define subjects and locations.

The following commands are examples of running the preprocessing steps:

...

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

FreeSurfer Preprocessing

Make sure each subject has a successfully completed FreeSurfer preprocessing set of files.

...