Hi Sergio - Thank you for your kind words, and also thank you for taking the time to search the archives for answers!
The first problems you had with running bedpostx through trac-all have to do with trac-all assuming an older version of FSL than the current one, and this'll be fixed in the upcoming release of trac-all. Indeed the thing to do in the meantime is to run bedpostx by itself, as you did. I apologize for the inconvenience.
About the problem you had when you ran bedpostx directly: do you get the other outputs of bedpostx, listed here? Are there any other, temporary files left over as well? http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_bedpostx.html
The merged_ph?samples are the orientation angles of the each of the two anisotropic compartments ("sticks", "fibers", whatever you want to call them) that bedpostx fit in each voxel. So "1" is the orientation angle of the largest stick/fiber, and "2" the one of the 2nd largest. If there's a "2", there should be a "1"!
Also, I looked at your dmrirc file and noticed that you decreased the # of control points b/c you hate waiting :) I just wanted to warn you that decreasing that # might make you wait longer b/c make fitting a spline with fewer control points to initialize the algorithm is sometimes more challenging.
Hope this helps, a.y
On Thu, 26 Jul 2012, Sergio Medina wrote:
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 listhttps://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024042.html I 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.
-- Sergio Medina Engineer INRIA Parietal - Neurospin Bât 145, Point Courrier 156 91191 Gif/Yvette, France Tel.: (+33) 1 69 08 80 85