This is because the mac executables in freesurfer where compiled on the
leopard verion of OSX. There's an update here compiled on snow leopard
that should solve this error:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula
On Thu, 16 Feb 2012, Tetiana Dadakova wrote:
Thanks for the note. I
Sorry for bothering you again,
I have another error now: Error: bvecs and bvals don't have the same
number of entries.
Visually my bval/bvec files seem ok to me. I can't find the problem.
I attach the files, could you please take a look on them?
Thank you very much,
Tanja.
On Tue, Feb 14, 2012
When I look at them with the more command on a linux machine, I see 2
lines in bval and 6 lines in bvec. Most likely this is a problem with the
text files being created with a windows program like excel and not having
unix-compatible end-of-line characters. It's been discussed a few times in
Dear Priti, Anastasia,
Thank you for your help, I created bvec and bval files and it went fine.
But now I have another error in preprocessing step.
I attach a log file. Could you please take a look at that?
Thank you,
Tanja.
trac-preproc exited with ERRORS at Fri Feb 10 10:52:37 CET 2012
You need to set the nb0 parameter (number of low-b volumes in the
beginning of your DWI series).
On Tue, 14 Feb 2012, Tetiana Dadakova wrote:
Dear Priti, Anastasia,
Thank you for your help, I created bvec and bval files and it went fine.
But now I have another error in preprocessing step.
PS: The info on what you need to set it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read from DICOM header
#
set nb0 = 10
On Tue, 14 Feb 2012, Tetiana Dadakova wrote:
Dear Priti, Anastasia,
Thank
I see, thank you :)
On Tue, Feb 14, 2012 at 6:50 PM, Anastasia Yendiki
ayend...@nmr.mgh.harvard.edu wrote:
PS: The info on what you need to set it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc
# Number of low-b images
# Must be specified if inputs are not DICOM
# Default: Read
Hi Tanja,
I think the problem may be due to the trailing slash you've included while
specifying $dtroot, $SUBJECTS_DIR etc.
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1/
should be
setenv SUBJECTS_DIR /Applications/freesurfer/subjects/TRACULA/T1
trac-all usually adds the
Hi Priti,
I changed the dmrirc file to the one you sent, but unfortunately got
the same error. I attach the log (although it is basically the same).
Do you have any ideas what else can cause it?
Thanks again,
Tanja.
On Fri, Feb 3, 2012 at 4:51 PM, Priti Srinivasan
rspr...@nmr.mgh.harvard.edu
Hi Tanja,
Can you check if the $dtroot/$subjectname/dmri/dwi_orig_flip.mghdti.bvecs
was created at all? It looks like that may not have been created and
that's why it can't find dwi_orig_flip.mghdti.bvecs. If your bvals and
bvecs information is not encoded in the dicom header, then you can
Hi Tanja,
It is supposed to be created automatically. Can you send your
configuration file and log file for us to see what's going on?
Thanks,
Priti
Dear list,
I try to run TRACULA pre-processing step and I get the following
error: /dmri/bvecs: No such file or directory.
I have a folder
Hi Tanja - The file is supposed to be created under
$dtroot/$subjectname/dmri/bvecs. If it's trying to create it as
/dmri/bvecs, this means that something wasn't defined correctly. What is
the exact trac-all command line that you're using? And your configuration
file if you're using one?
a.y
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