2012/7/26 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>

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.

Great! By any chance, do you know when that release will happen?

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

I have all of them, except for nodif_brain. And I only have the ones with i=2 while I should have the ones with i=1 too.
Attached you can find two files, the output of ls -Rah on both dmri and dmri.bedpostX directories.

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"!

But there are not :(

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.

Hehe, thanks! I changed it back to 5 now...

Thanks!

Sergio.

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

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