Hi Viviana - Does it die at that point or does it keep running? If it's
the latter it doesn't look wrong. For your first problem you should make
sure that your path includes the bin/ directory under the FSL
distribution.
a.y
On Wed, 25 Apr 2012, Viviana Siless wrote:
Hi Anastasia,
I ran:
Hi Anastasia,
I ran:
- bedpostx /media/vivi/images/freesurfer/00112288Proc/dmri
and got the following output:
subjectdir is /media/vivi/images/freesurfer/00112288Proc/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
But before it to
Hi Viviana - I cannot replicate this on our systems but I think I know
what your system may be fussy about and I'll amend it. For now, if you
don't get any outputs can you please try running bedpostx directly on
/media/vivi/images/freesurfer/00112288Proc/dmri and see if that works?
Thank
Hello Anastasia,
It fixed the bug. Thank you so much!
Now Im running trac-all -bedp -c
But it's been running for already 3 days, and it just printed that:
> trac-all -bedp -c /media/vivi/images/freesurfer/dmrirc.example
INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer
INFO: Diffusion root is
Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution MNI
template brain, and our atlas was built using the 1mm one. From your
dmrirc file:
# MNI template (the only option for inter-subject registration in this
version)
# Default: $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii
Hi Anastasia,
My mistake with the expiration date.
Please try with this link:
https://transfert.inria.fr/fichiers/0b1013b5de0fc0cc9e8dd2d6101a054b/testData.tar.gz
Thanks!
Viviana Siless
--
Parietal Team, INRIA Saclay
Neurospin, Centre CEA de Saclay
91191 Gif sur Yvette – FRANCE
On Tue, Apr 17,
Hi Anastasia,
Here is the data:
https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet
me know if you have any trouble.
I changed to the other track-all, and the error is the same.
Please let me know if I'm doing anything wrong!
Thank you!
Viviana Siless
--
Parieta
Hi Viviana - If you upload this data set I'm happy to look at it.
Also, I strongly recommend getting the updated version of trac-all from
the wiki (I'm guessing from the log file that you're probably not using
that?) See 2012/01/09 update here:
http://surfer.nmr.mgh.harvard.edu/fswiki
