Hi Amanda - Glad to hear the registration issue got fixed! If the tract looks like a single line in the volume (in which case you wouldn't be able to see it 3D in view), it's probably a case where the initialization failed for that specific tract and subject. This happens sometimes with the forceps major when there are enlarged ventricles or something like that. You can reinitialize by including "set reinit = 1" in your config file, setting the pathlist and subjlist to only the specific tract/subject that needs to be reinitialized, and then rerunning the -prior and -path steps in that order.
Hope this helps, a.y On Thu, 12 Feb 2015, Worker, Amanda wrote: > Hi Anastasia, > > Apologies this looks like an error on my part. I had edited the script to > specify --init-spm instead of --init-fsl but forgot to specify that this > script was to be used. It all seems to be looking good now which is > fantastic- thanks very much for all of your help!! > > One last question, when using the command: > > freeview -tv > $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/merged_avg33_mni_bbr.mgz \ > -v $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz & > > I am able to see all of the tracts clearly, except in some of the subjects > the Forceps Major seems to be missing. Changing the threshold doesn't seem to > make a difference. Do you have any ideas what the issue could be with this? > > Thanks, > > Amanda > > ________________________________________ > From: [email protected] > <[email protected]> on behalf of Anastasia Yendiki > <[email protected]> > Sent: 11 February 2015 16:21 > To: Freesurfer support list > Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error] > > Hi Amanda - It doesn't look like the new registration was applied to the > aparc+aseg. Can you tell us the exact sequence of steps that you followed, > including your bbregister command line and the trac-all command lines that > you ran after running bbregister? > > Thanks, > a.y > > On Wed, 11 Feb 2015, Worker, Amanda wrote: > >> Hi, >> >> Thanks for this. --init-spm does appear to work and when checking the >> registration using the instructions bbregister gives it all looks good to >> me. However, when I check the dtifit_FA and aparc+aseg.bbr.nii it still >> doesn't look too good. I've continued on with the next steps for >> reconstructing the pathways just to see what happens, but they don't come >> out well. >> >> I've attached a screenshot of the registration using --init-spm and then >> also a screenshot of the dmri/dtfit_FA.nii.gz alone and with >> aparc+aseg.bbri.nii overlayed. >> >> Best wishes, >> >> Amanda >> >> >> >> >> ________________________________________ >> From: [email protected] >> <[email protected]> on behalf of Douglas N Greve >> <[email protected]> >> Sent: 06 February 2015 19:15 >> To: Bruce Fischl; Freesurfer support list >> Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error] >> >> or --init-rr if you don't have matlab/spm >> >> On 02/06/2015 01:49 PM, Bruce Fischl wrote: >>> try --init-spm >>> On Fri, 6 Feb 2015, Anastasia Yendiki wrote: >>> >>>> >>>> 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: [email protected] >>>>> <[email protected]> on behalf of Anastasia >>>>> Yendiki <[email protected]> >>>>> 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: [email protected] >>>>>> <[email protected]> on behalf of Anastasia >>>>>> Yendiki <[email protected]> >>>>>> 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: [email protected] >>>>>>> <[email protected]> on behalf of Anastasia >>>>>>> Yendiki <[email protected]> >>>>>>> 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: [email protected] >>>>>>>> <[email protected]> on behalf of Anastasia >>>>>>>> Yendiki <[email protected]> >>>>>>>> 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: [email protected] >>>>>>>>> [[email protected]] on behalf of Anastasia >>>>>>>>> Yendiki [[email protected]] >>>>>>>>> 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 >>>>>>>>>> [email protected] 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: [email protected] >>>>>>>>>> <[email protected]> on behalf of Anastasia >>>>>>>>>> Yendiki <[email protected]> >>>>>>>>>> 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 >>>>>>>>>> [email protected] >>>>>>>>>> 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 >>>>>>>>>> [email protected] >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> [email protected] >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> [email protected] >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> [email protected] >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> [email protected] >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> [email protected] >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> [email protected] >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> [email protected] >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> [email protected] >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
