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 < > rspr...@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 >> >> <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 >> >> > _______________________________________________ >> >> > 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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
