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 < rspr...@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 < > > 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 > > > > -- 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 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.
