Hi Gari - Just looked at your subject. The bottom of the brain is
truncated in the DWIs. The slices stop in the middle of the angular
bundle, which is why the -prior step failed in that pathway. But I expect
there'd be problems with other tracts that reach that inferior, even if
they didn't fail completely - corticospinal, uncinate, inferior
longitudinal fasciculus.
a.y
On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia,
I was testing just with one subject and it finished the -prep part with
error.
Please find attached the trac-all.log file.
As this is a test user you will see some other invocations of trac-all. The
last build_stamp starts at row 54.500 aprox.
(just in case: I started new from de DICOMS and the dcm2nii, and I am using
the resulting .nii, .bvec and .bval, just in case I attached the dmrirc
too).
Thanks again for your help!
Gari
On Thu, Sep 26, 2013 at 8:01 AM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
Hi Gari - Yes, that's your best option right now. Sorry for the
inconvenience. I'll make sure to add the option to have one
gradient file per subject in the next version.
a.y
On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi! Thanks for the fast answer. If I do: diff
id1.bvec id2.bvec
I can see some clear differences.
I was told that in FSL I should use the bvecs and
bvals created in dcm2nii
per subject, so I understand I should do the same
now?
Do you think an option would be to script the
creation of a dmrirc file per
each subject and then launch as many trac-alls as
subjects?
Thanks again,
Gari
On Thursday, September 26, 2013, Anastasia Yendiki
wrote:
Hi Gari - Sorry, right now the assumption is
that the gradient
vectors are the same for all subjects. How
different are they?
a.y
On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga
wrote:
Hi Anastasia,I am setting up the dmrirc
file to run
Tracula. I am using
Siemens Dicoms, so I did not specify any
setting for
bval and bvec, but when
trac-all -prep starts running it gives
the following
error: mv: cannot stat
'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs':
No such file or
directory
Ok, so I understand that our problem is
that we
don't have MGH Siemens
Dicom.
So I used dcm2nii to convert it to .nii
files and
each conversion gives me a
SubjectID.bval and SubjectID.bvec. Every
.bval is
the same file, but every
.bvec file is a different one.
I can edit "set dcm_list = " to include
all the
newly created .nii files,
but
My question is:
- How can I specify every .bvec value
for every
subject? In the dmrirc file
everything I see is a "set bvecfile = "
option.
Thank you very much,
Gari
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