I only created a diff2anat.flt.mat file which replaced the old one. Do they all need to be recreated? If so, is that something I add to the command line?
On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki < ayend...@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 >> <ayend...@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 >> <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 <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<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 <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 >> >> -- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati
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