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

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