2012/7/27 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>

The monitoring script that bedpostx runs and tells you if things have or haven't finished properly can't always be trusted. So if that's the only error message you see, I wouldn't worry about it. Have the *ph1* and *th1* files appeared this time?

On Fri, 27 Jul 2012, Sergio Medina wrote:

What a coincide! Our teams have both chosen the same release cycle strategy
:P

I ran bedpostx_postproc and I've got so many errors that makes me think the
problem is before this step (see output in attached
n1-bedpostx-postproc.txt).

So, I ran again bedpostx on the dmri directory, which the first run *seemed*
to finish and didn't throw any error (I attached the output in the first
email).
This run did finish, and it did throw errors (full output in
n2-bedpostx-dmri.txt):

[...]
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: 276: No such process

Then I started wondering whether I do have the right data to actually run
bedpostx, so I run the script that checks that: bedpostx_datacheck, the
output (n3-bedpostx-datacheck.txt) doesn't show any signs of errors so I
would like to assume everything is ok with the input data...

Any idea?

Thanks, once again.

Sergio.

2012/7/27 Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>

Hi Sergio - As with any imminent new version release, it's
happening "soon". I'd say in a month, I'm just not sure a month
from when :P

The fact that the temporary files (everything with *slice* in
the name) are still in your bedpostx directory means that
bedpostx didn't finish running properly. You can try running the
last step of bedpostx and see if you get any error messages that
give you any clues:
bedpostx_postproc.sh
/volatile/tracula/results/Diff001/dmri

Normally this step merges the individual slices into volumes and
deletes the temporary files. If all else fails, I'd ask the FSL
gurus.

Hope this helps,
a.y

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 FreeSurfermailinglisthttps://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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--
Sergio Medina
Engineer
INRIA Parietal - Neurospin
Bât 145, Point Courrier 156
91191 Gif/Yvette, France
Tel.: (+33) 1 69 08 80 85

--
Sergio Medina
Engineer
INRIA Parietal - Neurospin
Bât 145, Point Courrier 156
91191 Gif/Yvette, France
Tel.: (+33) 1 69 08 80 85