18 May
2012
18 May
'12
1:18 p.m.
The other registration files depend on diff2anat. For example, diff2mni is composed of diff2anat and anat2mni. If you're using the old diff2mni, it's like you didn't change anything.
The -intra step creates all these. You need to edit the command that generates the diff2anat in your version of trac-preproc. Either comment that line out so that it runs everything but that, or change that line to the options that worked for you.
On Fri, 18 May 2012, Kiely Madhavan wrote:
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 ayendiki@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 <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 >> >> > _______________________________________________ >> >> > 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 -- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati-- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati