Hi everyone, I have a question about the way to co-register the FA imaging after QSIPrep and DTIfit with its white matter mask imaging. When I used fsl header to check their coordinate system information, they are in different space (as following).
Now, I wanna use flirt from FSL to register the FA imaging to T1w image. The code is as follows (T1w image is in the same space with white matter mask imaging):
flirt -in FA.nii.gz -ref T1w.nii.gz -interp trilinear -dof 12 -omat diff2struct_fsl.mat
transformconvert diff2struct_fsl.mat FA.nii.gz T1w.nii.gz flirt_import diff2struct_mrtrix.txt
mrconvert FA.nii.gz FA.mif
mrtransform FA.mif -linear diff2struct_mrtrix.txt -inverse registered_FA.mif
mrconvert registered_FA.mif registered_FA.nii.gz
After getting the registered nifti file, I checked the coordinate system with fsl header. The coordinate system is still in the different space and the coordinate system of output image is chaotic.
The following is the header information of each file.
white matter mask:
| qform_name | Scanner Anat |
|---|---|
| qform_code | 1 |
| qto_xyz:1 | -1.000000 0.000000 0.000000 96.000000 |
| qto_xyz:2 | 0.000000 -1.000000 0.000000 96.000000 |
| qto_xyz:3 | 0.000000 0.000000 1.000000 -78.000000 |
| 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 | Scanner Anat |
| sform_code | 0 |
| sto_xyz:1 | 0.000000 0.000000 0.000000 0.000000 |
| sto_xyz:2 | 0.000000 0.000000 0.000000 0.000000 |
| sto_xyz:3 | 0.000000 0.000000 0.000000 0.000000 |
| sto_xyz:4 | 0.000000 0.000000 0.000000 1.000000 |
| sform_xorient | Unknown |
| sform_yorient | Unknown |
| sform_zorient | Unknown |
FA.nii.gz:
| qform_name | Scanner Anat |
|---|---|
| qform_code | 1 |
| qto_xyz:1 | -1.300000 0.000000 0.000000 95.850006 |
| qto_xyz:2 | 0.000000 -1.300000 0.000000 102.550011 |
| qto_xyz:3 | 0.000000 0.000000 1.300000 -86.150002 |
| 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 | Scanner Anat |
| sform_code | 1 |
| sto_xyz:1 | -1.300000 0.000000 0.000000 95.850006 |
| sto_xyz:2 | 0.000000 -1.300000 0.000000 102.550011 |
| sto_xyz:3 | 0.000000 0.000000 1.300000 -86.150002 |
| 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 |
T1w.nii.gz:
| qto_xyz:1 | -1.000000 0.000000 0.000000 96.000000 |
|---|---|
| qto_xyz:2 | 0.000000 -1.000000 0.000000 96.000000 |
| qto_xyz:3 | 0.000000 0.000000 1.000000 -78.000000 |
| 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 | Scanner Anat |
| sform_code | 0 |
| sto_xyz:1 | 0.000000 0.000000 0.000000 0.000000 |
| sto_xyz:2 | 0.000000 0.000000 0.000000 0.000000 |
| sto_xyz:3 | 0.000000 0.000000 0.000000 0.000000 |
| sto_xyz:4 | 0.000000 0.000000 0.000000 1.000000 |
| sform_xorient | Unknown |
| sform_yorient | Unknown |
| sform_zorient | Unknown |
registered_FA.nii.gz:
| qform_name | Unknown |
|---|---|
| qform_code | 0 |
| qto_xyz:1 | 1.293750 0.000000 0.000000 0.000000 |
| qto_xyz:2 | 0.000000 1.296040 0.000000 0.000000 |
| qto_xyz:3 | 0.000000 0.000000 1.286560 0.000000 |
| qto_xyz:4 | 0.000000 0.000000 0.000000 1.000000 |
| qform_xorient | Left-to-Right |
| qform_yorient | Posterior-to-Anterior |
| qform_zorient | Inferior-to-Superior |
| sform_name | Unknown |
| sform_code | 1 |
| sto_xyz:1 | -1.293750 -0.001792 -0.000289 95.579117 |
| sto_xyz:2 | -0.000000 -1.296037 -0.000152 101.986671 |
| sto_xyz:3 | 0.000000 -0.002012 1.286560 -85.043640 |
| 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 |
Does anyone know why does it happen? Are there anything wrong with the flirt and MRtrix code? Or let me know if you have any suggestions.
Thank you!!! Looking forward to your reply:D