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
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