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
