Hi Kiely - Looks like you used flirt for the intra-subject registration,
so you can look in trac-all.log for the flirt command line that registers
diffusion to anatomical and play around with the parameters.
You can also use bbregister instead of flirt for the intra-subject
registration - it has the option to initialize with flirt or with SPM.
Hope this helps,
a.y
On Wed, 16 May 2012, Kiely Donnelly wrote:
Hi Priti - Thanks for your help. The inter-subject registration seems to
have run OK, but there must be something wrong with the intra-subject
registration. When I try to view it using freeview, it's completely dark - I
don't see a brain at all. Is there a way to troubleshoot this?
Thanks,
Kiely
On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan
<rspr...@nmr.mgh.harvard.edu> wrote:
Hi Kiely,
Have you checked your inter and intra subject registrations? The
control
points going off the dwi is not only for one paths but for all
the paths.
If the registration goes terribly wrong, this can happen. You
can take a
look at
/dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration
diff-anat)
and
/dmri/brain_anat_mni.nii.gz (For inter-subject registration
anat-mni)
I would start by checking that first.
Priti
> Hello--
>
> I have run Tracula successfully for ~75 healthy subjects.
However, the
> pathway reconstruction seems to fail for a handful of people.
I've
> attached
> the log file for one of these subjects. It appears that the
control points
> are not within the dwi. A similar problem occurred in a
subject with
> substantial signal loss in the dwi, but that doesn't seem to
be the case
> for this particular person. I have been creating the entire
set of tracts,
> but at this point, I'm only interested in the SLFt and SLFp.
>
> Thanks,
>
> Kiely
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--
Kiely M. Donnelly, M.A.
Doctoral Candidate, Clinical Neuropsychology
University of Cincinnati
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