1. What kind of input does Tracula expect? Can I input NIFTI /Analyze diffusion files as input?
2. Which format should my gradient directions be in?
Voxel co-ordinates like FSL's format. To see an example refer to this page (add a link to configuration file)
3. Can I use tracula if I have Diffusion scans from Philips/GE?
You can, but you need to get the bvecs/bvals information and input that in the correct format for it to work.
4. I can't find trac-all commands in my system? Where can I find it?
Tracula was released with Freesurfer 5.1 version. If you have an older version, you need to update your version, to be able to run tracula.
5. I would like to start by doing the tracula tutorial. Where can I access the tutorial data and the tutorial to go with it?
The tutorial data is available for download from here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data
The tutorials can be accessed here:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
6. I would like to run tracula with priors from CVS space, since I've run CVS registration for Diffusion voxel based analysis. Is that option available yet?
We're working on it. It will be made available soon.
7. Is there a way of defining our own ROIs and get tracts?
Tracula uses training sets that are manually labeled by neuroanatomists, for the 18 tracts using strict protocols from a paper that was published (add a link to wakana et al here). Hence it is not an exploratory analyses where you can define your own ROIs and get your tracts.
8. I get the following error when I run trac-all? What am I doing wrong ?
Error: bvecs and bvals don't have the same number of entries
The bvecs and bvals in your data should have 3 lines and 1 line, respectively, with the entries in each line being the same as the no. of volumes in your 4D DWI input.
Sometimes LOCALE settings can lead to different handling of decimal seperators by awk, which can cause certain commands in tracula to fail. To make sure that's not the case, check the following:
To check the LANG
setting in your terminal using the following command:
echo $LANG
If it is not en_US.UTF-8, then add the following to your .cshrc file:
%locale
LANG="de_CH.UTF-8"
LC_COLLATE="en_US"
LC_CTYPE="en_US"
LC_MESSAGES="en_US"
LC_MONTERARY="en_US"
LC_NUMERIC="en_US"
LC_TIME="en_US"
LC_ALL="en_US"
9. I have different bvecs for different subjects? Can I supply bvecslist in the configuration file or should I specify the bvecs accordingly for each subject?
Currently we do not have the option for specifying multiple bvecs within one configuration file. We hope to add that option in the future.
10. I have recons for my subjects that were done using an older version of Freesurfer. I've updated freesurfer to the latest version and would like to do tractography using tracula. Should I re-run recons for all my subjects