Hi Akvile - Sorry for the late response, I was out of town for a bit.
At first glance it looks like all the tracts are stuck where they're initialized. This might happen occasionally for a tract if initializing it is tricky (i.e., if the subject is not well aligned to the atlas, if the brain mask has a hole, etc), which is why the reinit option exists. But I've never seen it happen to all tracts, so something's fishy here.
If you upload all the tracula-related directories for this subject (dmri, dlabel, dpath, scripts), I'll take a look.
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
a.y
On Thu, 13 Sep 2012, Akvile Lukose wrote:
Hello Freesurfers,
I ran into a problem running TRACULA that I couldn't solve myself, and I would really appreciate if you could have a look.
I am running a FS 5.1 on mac os x 10.7.4 (intel 64bit) machine with 16GB RAM.
I extracted the bvals and bvecs with the dcm2nii converter and adjusted the format to what FS expects (scans acquired on a non-Siemens scanner).
I attach the dmrirc file as well.
First, I had a memory problem (cannot alloc memory) during the –prep stage. The new compiled update from here (http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula%C2%A0)helped and –prep stage finished without any errors.
I was not able to run bedpostx from dmrirc configuration file. I could work around it by running bedpostx directly on dmri directory (as described here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html). Then I had a problem with symlinks, I created them manually and after that it worked fine, I had all the output files as listed here (http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html).
-path worked also without any errors, but I keep getting very short thin tracks (all tracks) (snapshot attached). There is nothing wrong with the aparc+aseg.mgz. I tried rerunning every stage after I added option "set reinit=1" (as described here http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21990.html), but unfortunately it didn't help.
Do you have any ideas how to fix it? Thank you very much in advance!
Kind regards,
Akvile Lukose