16 May
2012
16 May
'12
11:12 a.m.
No, this is something you have to try yourself on the command line. If you want to make the change permanent, you can edit the relevant line in $FREESURFER_HOME/bin/trac-preproc.
On Wed, 16 May 2012, Kiely Donnelly wrote:
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