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
     >> >> > _______________________________________________
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     >> >> >
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     >> >>
     >> >>
     >> >>
     >> >> 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
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     >> you
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     >> >>
     >> >>
     >> >>
     >> >>
     >> >> --
     >> >> 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