Hi!
First of all let me thank you for having put at our disposal such great tools as FreeSurfer and Tracula! I am trying to run Tracula on the sample data that is on the website, but I've been running into some issues. I am attaching the configuration file just in case (dmrirc_single_subject-serch).
The first step "trac-all -prep" seems to run fine. The first problem comes with the second step "trac-all -bedp". The complete trace is included in the attached file 1-error-trac-all-bedp.txt After finding this on the FreeSurfer mailing list https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024042.htmlI changed the lines
*${BPDIR}/fsl_sub_seychelles*
for
*${FSL_BIN}/fsl_sub*
in the bedpostx_seychelles and I could continue, until the script seems to be stuck
*Queuing parallel processing stage /volatile/tracula/results/**Diff001/dmri.bedpostX/monitor 0 slices processed 1 slices processed 1 slices processed 1 slices processed <== this line keeps on repeating*
Following a suggestion I found on this other archived email http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html I ran bedpostx on the dmri directory and seemed to succeed. I am attaching the output (2-bedpostx-dmri.txt).
Then I tried to run trac-all -path but it stops with the following error:
*niiRead(): error opening file /volatile/tracula/results/** Diff001/dmri.bedpostX/merged_**ph1samples.nii.gz ERROR: Could not read /volatile/tracula/results/** Diff001/dmri.bedpostX/merged_**ph1samples.nii.gz*
I searched for that file everywhere but it doesn't exist. The closest I found was
results/Diff001/dmri.bedpostX/merged_ph2samples.nii.gz
Just in case I tried once again to run trac-all -bedp and this time, after having run bedpostx on the dmri directory, I get the following error (the whole output is in the attached 4-error-trac-all-bedp-2.txt file):
*[...] slice 62 has already been processed slice 63 has already been processed wc: /volatile/tracula/results/**Diff001/dmri.bedpostX/**commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 390: No such process*
I tried searching for a file named commands.txt but I couldn't find any.
Here is the output of bugr:
*FREESURFER_HOME: /i2bm/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.38-14-generic x86_64*
and the output of source $FREESURFER_HOME/SetUpFreeSurfer.sh
*-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /i2bm/local/freesurfer FSFAST_HOME /i2bm/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /volatile/tracula/data/buckner_data/tutorial_subjs/ MNI_DIR /i2bm/local/freesurfer/mni FSL_DIR /usr/share/fsl/4.1*
Thanks in advance for your help, any hint would be highly appreciated.
Best,
Sergio.