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 subjectregistration
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