We've generally seen better results with BBR, which is why it became the default setting.
On Thu, 6 Feb 2014, Jon Wieser wrote: > HI Anastasia, > > I ran it again with the flirt registration and it finished ok. > We did not have a specific reason for running it both ways. we are using the > default setting for the dmrirc file. > do you recommend one method over the other? > > thanks again > Jon > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> > To: "Jon Wieser" <wie...@uwm.edu> > Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> > Sent: Thursday, February 6, 2014 3:07:12 PM > Subject: Re: [Freesurfer] Fwd: trac-all -path error > > > That's entirely up to you, and whether you had a specific reason for > running it both ways. > > If you want to fix the bbr registration manually, check the trac-all.log > file for a command at the end of bbregister, where it says "To check > results, run". > > On Thu, 6 Feb 2014, Jon Wieser wrote: > >> Hi Anastasia, >> We used both flirt and bbr registration in the dmrirc file, the Aparc+seg >> I just showedd you was from the BBR resitration. I looked at the flirt >> registration. it looks OK. >> should I rerun tracula using only the flirt registration? >> Jon >> >> ----- Original Message ----- >> From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wie...@uwm.edu> >> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >> Sent: Thursday, February 6, 2014 11:00:25 AM >> Subject: Re: [Freesurfer] Fwd: trac-all -path error >> >> >> So there's your culprit. You need to fix the intra-subject >> (diffusion-to-T1) registration. Did you use flirt or bbregister for that? >> >> On Thu, 6 Feb 2014, Jon Wieser wrote: >> >>> Hi Anastasia, >>> I looked at the dlabel/diff/Aparc+aseg overlayed on the >>> dmri/dtifit_FA.nii.gz >>> the alignemenst is way off (in freeview, in the coronal view, the aparc+seg >>> is rotated 45 degrees anti-clockwise), and parts of the FA map in the L >>> ILF area are missing. the original DTI is not missing data in these areas. >>> I have attached screenshots >>> Jon >>> >>> >>> >>> ----- Original Message ----- >>> From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wie...@uwm.edu> >>> Cc: freesurfer@nmr.mgh.harvard.edu >>> Sent: Wednesday, February 5, 2014 6:35:12 PM >>> Subject: Re: [Freesurfer] Fwd: trac-all -path error >>> >>> >>> Hi Jon - You need to look at the aparc+aseg after it has been mapped to >>> diffusion space. It's possible that it looks fine in its original space >>> but then maybe something goes wrong with the registration. So you should >>> look at the aparc+aseg and aparc+aseg_mask files from the tracula >>> dlabel/diff directory. These are in diffusion space and you can overlay >>> them on the FA map to see if there's anything strange in the ILF area. >>> >>> Hope this helps, >>> a.y >>> >>> On Tue, 14 Jan 2014, Jon Wieser wrote: >>> >>>> Hi anastasia >>>> I looked at the brainmask and the aparc+aseg. I did see anything missing >>>> in the area of the left ILF. >>>> I have attached the files. can you take a look at them? >>>> Thanks >>>> JOn >>>> >>>> ----- Original Message ----- >>>> From: "Anastasia Yendiki" <ayend...@nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wie...@uwm.edu> >>>> Cc: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> >>>> Sent: Friday, January 10, 2014 6:15:23 PM >>>> Subject: Re: [Freesurfer] Fwd: trac-all -path error >>>> >>>> >>>> Hi Jon - Have you checked the brain mask and aparc+aseg for this subject? >>>> Anything missing there that might affect the left ILF? >>>> >>>> a.y >>>> >>>> On Wed, 8 Jan 2014, Jon Wieser wrote: >>>> >>>>> >>>>> Dear freesurfer experts >>>>> I'm getting the following error when runing trac-all -c >>>>> dmrirc_single_subject -path >>>>> >>>>> >>>>> Loading initial proposal SD's from >>>>> /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/Data/MRI/N1084/data/freesurfer/dlabel/diff/lh.ilf_AS_avg23_mni_flt_cpts_5_std.txt >>>>> Processing pathway 3 of 18... >>>>> Initializing MCMC >>>>> Segmentation fault >>>>> Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 >>>>> 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 >>>>> >>>>> >>>>> I have attached the trac-all.log and trac-all.error files >>>>> >>>>> I am running tracula 5.3 >>>>> >>>> >>>> >>>> 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. >>>> >>>> >> >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
