> 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
>> <
rspriti@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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>>
>>
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>>
>> --
>> Kiely M. Donnelly, M.A.
>> Doctoral Candidate, Clinical Neuropsychology
>> University of Cincinnati
>>
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