So far it isn't anymore. It's more of a problem with ANTs now. BBRegister works with --init-header for partial FoV T1 and mean EPI are more or less in alignment. But if they wouldn't be then one would have a problem with registration.
On 07/13/2017 12:35 AM, Douglas N Greve wrote: > Is this still a problem? > > On 07/11/2017 09:51 AM, Paul Glad Mihai wrote: >> Hi Bruce, >> >> Thanks for the quick reply. I've just finished rerunning it with spm, >> fsl and header init and the latter seemed to work if I write out a >> _bbreg.nii file. The former two failed, however. Apparently using the >> header seems to work for this one subject and one run. I'm testing the >> rest of the runs. >> >> This is an example from the FSL init. Please note that I'm running it >> through nipype, hence the jumbled subdirectory strucutre. >> >> bbregister --t2 --epi-mask --init-fsl --fslmat >> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat >> --reg >> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.dat >> --o >> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg.nii >> --mov >> /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/_init_fsl/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii >> --s sub-01 >> >> The output is attached. Details are under the heading 'Terminal output'. >> I'm also attaching a screenshot of the T2 with a white overlay for the >> header init. It seems to be alright. The output from the header init is >> also attached. The difference in the command line is --init-header >> instead of --init-fsl. >> >> Downstream, however, the registration to MNI through ANTs seems to fail, >> even though I've converted the transformation matrices to ITK through >> C3D. Hmmmm... I just had a revelation. I may have used the wrong T1 to >> calculate the registration matrix through ANTs. Instead of using the T1 >> from the ReconAll output, I used the one from the fsl.bet. I'll make >> sure to use the ReconAll T1 and get back to you. >> >> I would appreciate a comment, however, on how to get better registration >> of partial FoV T2 images to T1 images through BBRegister. It seems that >> the easiest option is a full head EPI at the time of the experiment. >> >> Regards, >> Glad >> >> >> >> On 07/11/2017 03:33 PM, Bruce Fischl wrote: >>> Hi Glad >>> >>> can you send us the full command line you are using and screen output? >>> >>> thanks >>> >>> Bruce >>> On >>> Tue, 11 Jul 2017, Paul Glad Mihai wrote: >>> >>>> Dear List, >>>> >>>> I've been quite frustrated with the BBRegister results when trying to >>>> register a partial field of view EPI mean functional image to a T1 scan. >>>> I've tried different init arguments (fsl, spm, header) and none really >>>> work. I've found that the initial registration is causing the problem, >>>> since the T1 and mean EPi are in reasonable alignment, but not perfect. >>>> As soon as it passes the initial alignment it's totally off and >>>> obviously fails in the BBR step. I have no full head EPI, unfortunately. >>>> I have a full head scout which seems to be a T1 image with really poor >>>> contrast. If I try to register this to the T1 through BBRegister it >>>> works. But if I use it as an intermediate file it still fails. What can >>>> I do? How does the intermediate file come into play? Will it get >>>> registered to the T1 initially and then the resulting matrix is used >>>> further? I also tried to feed the resulting registration matrix as >>>> init-reg but that didn't work either. >>>> >>>> Is there a way to skip the initial registration? >>>> >>>> Can I mask the T1 image with the FoV of the functional scan if they are >>>> initially in reasonable alignment? Would that work? Would that mean that >>>> I have to re-run ReconAll with the masked T1? >>>> >>>> Would love to hear back from someone. >>>> >>>> Regards, >>>> Glad >>>> >>> _______________________________________________ >>> 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 > -- Paul Glad Mihai, PhD Independent Research Group "Neural Mechanisms of Human Communication" Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A, 04103 Leipzig, Germany Phone: +49 (0) 341-9940-2478 E-mail: [email protected] _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
