Hello Experts, Just to follow up on my previous posting, here is the information from the headrs of the different nifti files after the steps performed.
* First, the header of the mean original nifti after realignment: qto_xyz:1 -1.099422 0.024665 0.025745 65.286888 qto_xyz:2 -0.021598 -1.092710 0.124570 38.997047 qto_xyz:3 0.028368 0.123999 1.092621 -26.324900 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient Anterior-to-Posterior qform_zorient Inferior-to-Superior sform_name Aligned Anat sform_code 2 sto_xyz:1 -1.099422 0.024662 0.025746 65.286888 sto_xyz:2 -0.021594 -1.092710 0.124570 38.997047 sto_xyz:3 0.028368 0.123999 1.092621 -26.324900 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Anterior-to-Posterior sform_zorient Inferior-to-Superior * Second, the header of the nifti after bbregister with the write output option enabled: qto_xyz:1 -1.000000 0.000000 -0.000000 126.995163 qto_xyz:2 0.000000 0.000000 1.000000 -135.546768 qto_xyz:3 -0.000000 -1.000000 -0.000000 109.658028 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient Superior-to-Inferior qform_zorient Posterior-to-Anterior sform_name Scanner Anat sform_code 1 sto_xyz:1 -1.000000 0.000000 0.000000 126.995163 sto_xyz:2 0.000000 0.000000 1.000000 -135.546768 sto_xyz:3 0.000000 -1.000000 0.000000 109.658028 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Superior-to-Inferior sform_zorient Posterior-to-Anterior * This is the matrix (.mat) resulting from the bbregister step: -0.99996966 0.00760214 -0.00178158 192.10556030 0.00103370 -0.09726234 -0.99525851 135.02107239 -0.00773941 -0.99522978 0.09725130 173.68141174 0.00000000 0.00000000 0.00000000 1.00000000 * Third, the header of the nifti after mri_vol2vol using the matrix from the bbregister step: qto_xyz:1 0.000000 0.000000 0.700000 -85.004837 qto_xyz:2 -0.700000 0.000000 0.000000 104.453209 qto_xyz:3 0.000000 -0.700000 0.000000 93.658028 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Anterior-to-Posterior qform_yorient Superior-to-Inferior qform_zorient Left-to-Right sform_name Scanner Anat sform_code 1 sto_xyz:1 0.000000 0.000000 0.700000 -85.004837 sto_xyz:2 -0.700000 0.000000 0.000000 104.453209 sto_xyz:3 0.000000 -0.700000 0.000000 93.658028 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Anterior-to-Posterior sform_yorient Superior-to-Inferior sform_zorient Left-to-Right Regards, Glad On 07/13/2017 11:02 PM, Paul Glad Mihai wrote: > Hello, > > I'm getting two different results from the coregistration step. When I run > bbregister on the mean epi it coregisters properly and writes out _bbreg.nii. > The next step involves registering the realigned epi time series to the T1 > image using the same transform matrix calculated from the mean image. But the > results fail miserably. I've attached some sample images. > > I came across the same result after transforming the matrix it to ITK space > and applying the transform using ANTs' applyTransform, which tells me that > the ITK conversion works, but this registration goes wrong. Or I may not > really understand what I'm doing, lol. > > Here are the commands: > > bbregister --t2 --epi-mask --init-header --fslmat > /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/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/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/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/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold.nii > --s sub-01 > > mri_vol2vol --fsl > /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/bbreg/mapflow/_bbreg0/meanusub-01_task-spespk_run-01_bold_bbreg_sub-01.mat > --mov > /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold.nii > --targ > /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/brainextract/sub-01_acq-T1w_brain.nii.gz > --o > /data/pt_nmc002/TDMGB_FMRI_coreg/tmp/preproc/_subject_id_sub-01/coreg_func/mapflow/_coreg_func0/usub-01_task-spespk_run-01_bold_warped.nii > > Regards, > Glad > > > > _______________________________________________ > 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. > -- 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: mi...@cbs.mpg.de _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
