You may have to give up the arcuate (slft) too, since part of the temporal
lobes are chopped off. Although it didn't get to that tract so it's just a
guess.
Yes, you should be fine by removing from pathlist (and the respective
entries in ncpts) any tracts that are partly cut off in your images.
The registrations are fine, bbregister managed to align the DWI to the T1
even though only the former is truncated. And the registration to the
atlas uses the T1, so that worked fine too.
Hope this helps,
a.y
On Fri, 27 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Many thanks Anastasia. So, do you think it would work if I exclude this
tracts from the analysis and ask for the remaining ones?
thanks again,
Gari
On Fri, Sep 27, 2013 at 4:35 PM, Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu> wrote:
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
The information in this e-mail is
intended
only for the person
to whom it is
addressed. If you believe this
e-mail was sent
to you in error
and the e-mail
contains patient information,
please contact
the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If
the e-mail was sent
to you in error
but does not contain patient
information,
please contact the
sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
