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
