I have edited the trac-preproc script to "--init-header" instead of "--init-fsl" - hoping that this would fix the registration problem. Perhaps this hasn't helped? ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> Sent: 12 January 2015 19:58 To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA mask error
Have you checked that the registration has been fixed? It looks like it might not. On Mon, 12 Jan 2015, Worker, Amanda wrote: > Yes of course. Please find attached. > > Thanks, > > Amanda > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki > <ayend...@nmr.mgh.harvard.edu> > Sent: 12 January 2015 16:39 > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA mask error > > Can you please attach the entire trac-all.log file? It's hard to tell just > from the last few lines, the initial error may have happened much earlier. > > On Mon, 12 Jan 2015, Worker, Amanda wrote: > >> Hi Anastasia, >> >> Thank you for your response. I have made the changes that you recommended >> and attempted to run trac-all -prep on one of the subjects with errors. I am >> now getting the following error: >> >> Writing output files to >> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_* >> Writing spline volumes to >> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz >> Segmentation fault >> >> trac-preproc-edit exited with ERRORS at Fri Jan >> >> >> Do you have any idea what the problem could be now? >> >> Thanks, >> >> Amanda >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: 07 January 2015 17:11 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA mask error >> >> Hi Amanda - See attached screenshot of your data, there is a gross >> misregistration (~45 degree angle rotation) between the diffusion and >> anatomical. You can check if this is the case for the rest of your bad >> cases by superimposing the FA map (dmri/dtifit_FA.nii.gz) and anatomical >> segmentation mapped to diffusion space (dlabel/diff/aparc+aseg.bbr.nii). >> >> According to bbregister czar Doug, a big error like this in bbregister >> happens when the initialization of the registration fails. If the >> diffusion and T1 were acquired in the same session, you can try >> initializing the registration from the headers of the images, by running >> bbregister with "--init-header" instead of "--init-fsl". >> >> You can try it on one of your subjects first. Search for the bbregister >> command line in trac-all.log of this subject and rerun bbregister with the >> changed option. Follow the instructions that bbregister prints out when >> it's done to check the registration. >> >> To change how tracula does this, you'll have to edit the script >> $FREESURFER_HOME/bin/trac-preproc >> Search for "bbregister" and edit the --init-fsl option. Then rerun >> trac-all for the subjects that had this problem. You can skip the first 2 >> steps of the preprocessing, i.e., do trac-all -prep -nocorr -noqa. >> >> Hope this helps, >> a.y >> >> PS: Yes, when you send something with filedrop that I should look at, give >> my email address as the recipient. >> >> >> On Wed, 7 Jan 2015, Worker, Amanda wrote: >> >>> Hi Anastasia, >>> >>> Thanks for your response. I have sent over a zip file via the filedrop >>> portal, it seemed to fail each time I tried to send it to >>> freesurfer@nmr.mgh.harvard.edu so I've sent it over to your email >>> address - hopefully you have received this. >>> >>> I've had a look at the segmentations and they look ok, so I think there >>> may be an issue with registrating between the T1 and diffusion. Anyway I >>> have sent an example over, hopefully this will give you some idea of >>> what has gone wrong. >>> >>> Thanks, >>> >>> Amanda >>> >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki >>> <ayend...@nmr.mgh.harvard.edu> >>> Sent: 11 December 2014 19:37 >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] TRACULA mask error >>> >>> Hi Amanda - The final masks used by tracula are derived from the >>> structural and not the diffusion data, i.e., they are the whole-brain >>> FreeSurfer segmentations (from mri/aparc+aseg.mgz) mapped onto diffusion >>> space and dilated slightly. It may be that there was something wrong with >>> the FreeSurfer reconstructions of those subjects (if, for example, the T1 >>> contrast was poorer in part of the brain and the part was not included in >>> the brain mask), or that there was misregistration between the T1 and >>> diffusion. You can troubleshoot this by looking at the aparc+aseg in >>> diffusion space (from the dlabel/diff directory, over the FA map (from the >>> dmri directory). >>> >>> If you still have trouble deciding what went wrong, you can upload a zip >>> file for me with all the directories created by trac-all (dmri, dlabel, >>> etc) for one of these subjects, here: >>> https://gate.nmr.mgh.harvard.edu/filedrop2/ >>> >>> Best, >>> a.y >>> >>> On Thu, 27 Nov 2014, Worker, Amanda wrote: >>> >>>> >>>> Dear All, >>>> >>>> >>>> I have run all of the pre-processing steps on my DTI data and as I am >>>> checking my nodif_brain_mask I have realised that some of the masks have >>>> become distorted and twisted in some way. I have attached screenshots of >>>> both the raw data (which looks fine) and the white mask (which is >>>> distorted). In addition, as I have read that it is important to check the >>>> dtifit_V1 and dtifit_FA I have also included these in the word document, >>>> incase this helps. >>>> >>>> >>>> This distortion has occured for approximately a quarter of the subjects >>>> that >>>> I have processed and the rest look good. Please can you let me know if you >>>> have any ideas about what has gone wrong and how to fix this? >>>> >>>> >>>> Thanks in advance for your help, >>>> >>>> >>>> Amanda >>>> >>>> >>>> >>> _______________________________________________ >>> 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. >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
