Can you please check that the x-y-z dimensions of the bedpostx output
files are the same as the dimensions of the DWIs?
On Thu, 23 Aug 2012, Natalia Sánchez wrote:
Thanks for your response!Attached are the requested files
The error occurs here are shown on my terminal:
Loading b-values
from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv
als
Loading gradients
from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv
ecs
Segmentation fault
Darwin dhcp-165-124-9-141.phystherapy.northwestern.edu 10.8.0 Darwin Kernel
Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011;
root:xnu-1504.15.3~1/RELEASE_I386 i386
-- Natalia Sánchez
PhD Candidate
Departments of Biomedical Engineering &
Physical Therapy and Human Movement Sciences Northwestern University
645 North Michigan Ave, Suite 1100
Chicago, IL 60611
On Thu, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Natalia - I'd need to see at which point in the processing
the error occurs, since this is a very generic error message.
Can you please include your trac-all.log and dmrirc?
Thanks,
a.y
On Thu, 23 Aug 2012, Natalia Sánchez wrote:
Hi Anastasia!I finally made tracula -prep work
without errors, using the 1mm
T1 MNI template (i tried using the 2mm one but the
vertices for registering
white matter came out as NaN). However, I was not
able to get bedpost to
work. After looking at other posts on the FS
archive, I think the reason why
-bedp does not work is because of my FSL version. I
tried running bedpost on
FSL and then just copying those files on my
dmri.bedpost folder and using
those files for reconstructing the white matter
tracts. However, I get a
"Segmentation Fault" error. Do you have any idea
what this error may mean?
My dpath folder is empty and I my trac-all.log file
has no errors related to
-path
Thanks!
-- Natalia Sánchez
PhD Candidate
Departments of Biomedical Engineering &
Physical Therapy and Human Movement Sciences
Northwestern University
645 North Michigan Ave, Suite 1100
Chicago, IL 60611
On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Natalia - This is an error that will occur
if lowb_brain_mask
does not exist. The command that generates
lowb_brain_mask is
"bet" - can you find that line in the log file
and run it
directly on the command line and see if you
get an error?
On a separate note, have you opted to use a
DWI mask instead of
an anatomical mask by setting usemaskanat = 0?
If not, then it
may be that it's trying to use the DWI mask
b/c it can't find
the anatomicals, in which case I'd check if
SUBJECTS_DIR has
been set properly and a freesurfer recon of
the same subject
exists there. But this is a separate
issue than the DWI mask not being generated.
Hope this helps,
a.y
On Fri, 10 Aug 2012, Natalia Sánchez wrote:
The required files were not generated.
the error occurs at
rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subjects
/Justin/cJD/dlabel/mni/low
b_brain
_mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/d
mri/mni/dtifit_F
A.fl
t.nii.gz --ncpts 5 --trunc --debug
ERROR: fio_pushd:
/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni
ERROR: Must specify brain mask volume for
output subject
does the brain mask have to be input manually
in the
configuration file, or
is this part of the pre-processing? since I
set the bet
thr to 0.23 in the
config file i thought the brain mask was also
created
during the
preprocessing stage. Attached is my log file.
I am familiar with FSL but I am using Free
surfer since i
think automating
the entire process, including tracking is a
great
advantage, but I'm just
starting to get the hang of it
Thanks!
-- Natalia Sánchez
PhD Candidate
Departments of Biomedical Engineering &
Physical Therapy and Human Movement
Sciences
Northwestern University
645 North Michigan Ave, Suite 1100
Chicago, IL 60611
On Fri, Aug 10, 2012 at 4:28 PM, Anastasia
Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
dtifit_FA.fl
t.nii.gz
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