On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:
Were the old .mat files replaced with the new ones?
On Fri, 18 May 2012, Kiely Madhavan wrote:
That seemed to fix the registration issue, but I'm still unable to
reconstruct the tracts using trac-all -path. I'm getting the same error that
the control points are not within the mask. THis happens for all tracts.
Thanks,
Kiely
On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki
<ayendiki@nmr.mgh.harvard.edu> wrote:
The .mat registration matrix should be saved under dmri/xfms/.
On Wed, 16 May 2012, Kiely Donnelly wrote:
I tried using corratio and it seems to have fixed
the registration issue.
I'm very new to this so just want to make sure I did
it correctly before I
move forward. Should the command line look something
like this if I am
running it in this individuals dmri directory:
flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz
-out
lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat
-cost corratio
Thanks so much for your help.
Kiely
On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan
<rspriti@nmr.mgh.harvard.edu> wrote:
you have to run flirt commandline separately to
check if it
solves your
problem.
> Is this something I can change in my dmrirc
file or do I need
to run flirt
> on it's own?
>
> Thanks,
>
> Kiely
>
> On Wed, May 16, 2012 at 9:27 AM, Priti
Srinivasan <
> rspriti@nmr.mgh.harvard.edu> wrote:
>
>> Kiely, For flirt, try using corratio, cost
function instead
of
>> mutualinfo
>> (which is the default in trac-all) to see if
that solves your
>> registration
>> problem.
>>
>>
>> > 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
>> >> >
_______________________________________________
>> >> > 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.
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> Kiely M. Donnelly, M.A.
>> >> Doctoral Candidate, Clinical
Neuropsychology
>> >> University of Cincinnati
>> >>
>>
>>_______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>
>
> --
> Kiely M. Donnelly, M.A.
> Doctoral Candidate, Clinical Neuropsychology
> University of Cincinnati
>
--
Kiely M. Donnelly, M.A.
Doctoral Candidate, Clinical Neuropsychology
University of Cincinnati
--
Kiely M. Donnelly, M.A.
Doctoral Candidate, Clinical Neuropsychology
University of Cincinnati