Hi Amanda - So it looks like --init-header didn't work, and neither does --init-fsl. I'll defer to the father of bbregister, Doug, for clues about how to proceed.
a.y On Wed, 21 Jan 2015, Worker, Amanda wrote: > Hi Anastasia, > > Yes I have done that. My command line was... " bbregister --s PDPLUS010 > --init-header --dti --mov > /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/dwi.nii.gz > --reg > /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/anatorig2diff.bbr.dat > --fslmat > /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/diff2anatorig.bbr.mat > " > > Following the instructions printed I can only see a tiny bit of the > dwi.nii.gz, as attached. > > I've also tried substituting --dti for --t1 in the command line and that > doesn't make much difference. > > Do you have any other ideas? > > 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: 15 January 2015 15:36 > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA mask error > > Did you follow the instructions and the end of the output of the > bbregister command? What does that look like? See what I wrote below about > looking for the bbregister command in trac-all.log, running it separately > on one subject after changing that one option and looking at its output. > > On Wed, 14 Jan 2015, Worker, Amanda wrote: > >> 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 > _______________________________________________ > 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
