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
Stephanstra├če 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

Reply via email to