Dear Manuel,
many thanks for the quick answer!
I tried remaming the partial volume mask as T1_BET_wmseg.nii.gz but unfortunately the error still remained (blue is 5tt_nocoreg.mif, orange is 5tt_coreg.mif
mrinfo says:
> ************************************************
> Image: "5tt_coreg_wmseg.mif"
> ************************************************
> Dimensions: 192 x 195 x 245 x 5
> Voxel size: 0.700521 x 0.7 x 0.700521 x ?
> Data strides: [ 2 -4 3 1 ]
> Format: MRtrix
> Data type: 32 bit float (little endian)
> Intensity scaling: offset = 0, multiplier = 1
> Transform: 0.9962 -0.08495 0.01874 -3.205
> 0.05217 0.7558 0.6527 -155.2
> -0.06962 -0.6493 0.7574 -35.24
> command_history: /home/duzzo/mrtrix3/bin/mrcalc "T1_BET_pve_1.nii.gz" "multiplier_noNAN.mif" "-mult" "remove_unconnected_wm_mask.mif" "-mult" "cgm.mif" "-nthreads" "4" (version=3.0_RC3-137-g5d6b3a6f)
> [6 entries] /home/duzzo/mrtrix3/bin/mrcat "cgm.mif" "sgm.mif" "wm.mif" "csf.mif" "path.mif" "-" "-axis" "3" "-nthreads" "4" (version=3.0_RC3-137-g5d6b3a6f)
> ...
> /home/duzzo/mrtrix3/bin/mrconvert "result.mif" "/mnt/226AE1226AE0F407/DTI/pipeline_test/Duzzo/5tt_nocoreg.mif" "-nthreads" "4" (version=3.0_RC3-137-g5d6b3a6f)
> mrtransform "5tt_nocoreg.mif" "-linear" "diff2struct_mrtrix_wmseg.txt" "-inverse" "5tt_coreg_wmseg.mif" "-force" (version=3.0_RC3-137-g5d6b3a6f)
> comments: 6.0.1
> transform modified
> mrtrix_version: 3.0_RC3-137-g5d6b3a6f
I then tried with a binary mask from 5tt image itself:
mrconvert 5tt_nocoreg.mif 5tt_nocoreg.nii.gz
fslsplit 5tt_nocoreg.nii.gz vol -t
mv vol0002..nii.gz T1_BET_wmseg.nii.gz
....
and the alignment improved (still not optimal):
mrinfo says:
Image: "5tt_coreg_wmseg.mif"
************************************************
Dimensions: 192 x 245 x 195 x 5
Voxel size: 0.700521 x 0.700521 x 0.7 x ?
Data strides: [ 2 3 4 1 ]
Format: MRtrix
Data type: 32 bit float (little endian)
Intensity scaling: offset = 0, multiplier = 1
Transform: 0.9959 -0.03314 -0.08453 -63
-0.003852 0.9147 -0.404 -56.37
0.09071 0.4027 0.9108 -77.84
command_history: /home/duzzo/mrtrix3/bin/mrcalc "T1_BET_pve_1.nii.gz" "multiplier_noNAN.mif" "-mult" "remove_unconnected_wm_mask.mif" "-mult" "cgm.mif" "-nthreads" "4" (version=3.0_RC3-137-g5d6b3a6f)
[6 entries] /home/duzzo/mrtrix3/bin/mrcat "cgm.mif" "sgm.mif" "wm.mif" "csf.mif" "path.mif" "-" "-axis" "3" "-nthreads" "4" (version=3.0_RC3-137-g5d6b3a6f)
...
/home/duzzo/mrtrix3/bin/mrconvert "result.mif" "/mnt/226AE1226AE0F407/DTI/pipeline_test/Duzzo/5tt_nocoreg.mif" "-nthreads" "4" (version=3.0_RC3-137-g5d6b3a6f)
mrtransform "5tt_nocoreg.mif" "-linear" "diff2struct_mrtrix_wmseg.txt" "-inverse" "5tt_coreg_wmseg.mif" "-force" (version=3.0_RC3-137-g5d6b3a6f)
comments: 6.0.1
transform modified
mrtrix_version: 3.0_RC3-137-g5d6b3a6f
so this surely has helped but has not solved the issue.
I’m also wondering why the 5tt_nocoreg.mif image is so similar to the mean_b0_preprocessed_BET.mif reference