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Hello,
I am trying to replicate the processing steps that occur between when a T1 is given as input to recon-all and the T1.mgz that is stored in the $SUBJECTS_DIR/$SUBJECT/mri directory for mne-bids and dealing with mne's internal dependency on the surface RAS coordinate frame.
It is my impression that 1) the image is resampled to 256 x 256 x 256 and then 2) the image is reoriented to head-first supine aka LIA aka scanner space. But when I replicate these steps using nibabel, the affine is off by a rotation and translation:
T1.mgz ------
[[ -1. , -0.00000015, -0.00000003, 132.77600098], [ 0.00000003, 0.00000001, 1. , -94.00223541], [ -0.00000002, -1.00000012, -0.00000001, 149.55487061], [ 0. , 0. , 0. , 1. ]]
orig resampled and translated -----------------------------
[[ -0.99995208, -0.00905184, 0.00373623, 164.44344257], [ 0.00337327, 0.03978604, 0.99920255, -98.49012464], [ 0.00919327, -0.9991672 , 0.03975359, 141.93864847], [ 0. , 0. , 0. , 1. ]]
orig to T1.mgz transform affine -------------------------------
[[ 0.99995203, -0.00337331, -0.00919312, -30.68693093], [ 0.0037362 , 0.99920251, 0.03975359, -1.8476189 ], [ 0.00905186, -0.03978605, 0.99916736, 2.32735433], [ 0. , 0. , 0. , 1. ]]
Since there are off-diagonal entries in the last affine, I assume there is some kind of rotation, and since there are non-zero entries in the last column, I assume there is some kind of translation as well. I am not sure what either of those would be from so any advice or help would be appreciated.
Alex Rockhill PhD Candidate University of Oregon
We refer to this operation as "conforming". This page might help https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 7/4/2021 4:39 PM, Alexander Rockhill wrote:
External Email - Use Caution
Hello,
I am trying to replicate the processing steps that occur between when a T1 is given as input to recon-all and the T1.mgz that is stored in the $SUBJECTS_DIR/$SUBJECT/mri directory for mne-bids and dealing with mne's internal dependency on the surface RAS coordinate frame.
It is my impression that 1) the image is resampled to 256 x 256 x 256 and then 2) the image is reoriented to head-first supine aka LIA aka scanner space. But when I replicate these steps using nibabel, the affine is off by a rotation and translation:
T1.mgz
[[ -1. , -0.00000015, -0.00000003, 132.77600098], [ 0.00000003, 0.00000001, 1. , -94.00223541], [ -0.00000002, -1.00000012, -0.00000001, 149.55487061], [ 0. , 0. , 0. , 1. ]]
orig resampled and translated
[[ -0.99995208, -0.00905184, 0.00373623, 164.44344257], [ 0.00337327, 0.03978604, 0.99920255, -98.49012464], [ 0.00919327, -0.9991672 , 0.03975359, 141.93864847], [ 0. , 0. , 0. , 1. ]]
orig to T1.mgz transform affine
[[ 0.99995203, -0.00337331, -0.00919312, -30.68693093], [ 0.0037362 , 0.99920251, 0.03975359, -1.8476189 ], [ 0.00905186, -0.03978605, 0.99916736, 2.32735433], [ 0. , 0. , 0. , 1. ]]
Since there are off-diagonal entries in the last affine, I assume there is some kind of rotation, and since there are non-zero entries in the last column, I assume there is some kind of translation as well. I am not sure what either of those would be from so any advice or help would be appreciated.
Alex Rockhill PhD Candidate University of Oregon
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Alexander Rockhill -
Douglas N. Greve