Hi Anastasia and the freesurfer list,
I've been working on getting the latest version of tracula to run and I thought I would post here the errors that I've worked around. It's all been based on looking through the mailing list archives but I thought it would be useful to add them here all in one place! The goal of this email is simply to save time for others in the future (including myself when I forget all these things!)
[Note that if I've written something between < > then it will be specific to your files/directories etc]
When running trac-all on an input nii file with corresponding bval and bvec files:
1) If you're getting an error that says:
nifti1Read(): unsupported slice timing pattern 5 in <NAME OF YOUR DTI NIFTI FILE>
Try running the command:
fslmaths <NAME OF YOUR DTI NIFTI FILE> <NAME OF YOUR DTI NIFTI FILE>
eg: fslmaths dti.nii.gz dti.nii.gz
I'm really not clear on what exactly is wrong with my files (created using an in house dicom converter) but taking in the file and writing it straight back out again gets rid of this problem for me.
2) If you're getting an error that says
ERROR: Could not open <SUBJECTS_DIR>/<SUBID>/dmri/bvals for reading
Then you're probably using the centos4 update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options - if the centos6 update works then switch to that, otherwise all other steps in trac-all -prep work *except* for the quality control. So you can run trac-all -prep -noqa and all should be well.
To install the update just download it (I used wget <TRACULA_UPDATE_LINK>) and the untar it (tar -zxvf <TRACULA_UPDATE_TAR.GZ_FILE>). Copy the files inside the folder you've created into the $FREESURFER_HOME/bin/ directory.
3) If you're getting an error that says (something along the lines of)
mri_convert --frame 0 14 27 41 54 68 <SUBJECTS_DIR>/<SUBID>/dmri/dwi.nii.gz <SUBJECTS_DIR>/<SUBID>/dmri/lowb.nii.gz
mri_convert: extra arguments ("41" and following)
type mri_convert -u for usage
Then you're probably using an old version of trac-all. Double check that you've replaced the appropriate files in your $FREESURFER_HOME/bin directory with those contained in the appropriate update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. (See my instructions at point 2).
Some fun facts from my experience: You can have decimal points (not commas though) in your bvals files. You can run trac-all in either a bash or tcsh shell. (These were not the droids I was looking for)
Thanks again for the really excellent software. And please correct anything that I've written here if it's wrong!
Kx