On Fri, 27 Jul 2012, Sergio Medina wrote:
Anastasia,
Thanks for such a quick reply!
Please find my answers inline...
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 mailinglisthttps://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
Bāt 145, Point Courrier 156
91191 Gif/Yvette, France
Tel.: (+33) 1 69 08 80 85
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--
Sergio Medina
Engineer
INRIA Parietal - Neurospin
Bāt 145, Point Courrier 156
91191 Gif/Yvette, France
Tel.: (+33) 1 69 08 80 85