Sorry, I misunderstood. I've attached a screenshot of what I can see, it does look like there is probably a different problem now as both the dtifit_FA.nii.gz and aparc+aseg.bbr.nii are completely off centre.
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: 13 January 2015 17:52 To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA mask error It's impossible to know unless you actually check the registration. See my previous email below on how to do that. On Tue, 13 Jan 2015, Worker, Amanda wrote: > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
registration screenshot.docx
Description: registration screenshot.docx
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