Image corregistration error in ACT with 5tt and dw image

[Alex_Sphyrna]

Hello, first time posting a question here!
I’m not an experienced user in any form, so sorry if I’m missing any obvious information.
I have this slight issue in which I’m trying to corregister a 5tt image with a DW image. The issue is with mixed planes in the incorrect axis.

The code that Im using is the one implemented in the BATMAN tutorial:

5ttgen fsl T1_raw.mif 5tt.mif

dwiextract dwi_bias.mif - -bzero | mrmath - mean mean_b0_preproc.mif -axis 3

mrconvert mean_b0_preproc.mif mean_b0_preproc.nii.gz

mrconvert 5tt.mif 5tt.nii.gz

flirt -in mean_b0_preproc.nii.gz -ref 5tt.nii.gz -interp nearestneighbour -dof 6 -omat diff2struct_sfl.mat

transformconvert diff2struct_sfl.mat mean_b0_preproc.nii.gz 5tt.nii.gz flirt_import diff2struct_mrtrix.txt

mrtransform 5tt.mif -linear diff2struct_mrtrix.txt -inverse 5ttf.mif

The only image that exhibits this property is the final 5tt image, hence: 5ttf.mif, created in the mrtransform line.

Anyway, thanks for any help anyone may provide!

[jdtournier]

I also found that particular step not to work too well. There’s a few alternative approaches there, but one I found seemed worked OK was to register the mean b=0 image to the GM parcel from the 5TT image, using linear interpolation (not nearest-neighbour), and ensuring the strides match (and are NIfTI standard). This looks like this:

...
mrconvert mean_b0_preproc.mif -stride 1,2,3 mean_b0_preproc.nii.gz
mrconvert 5tt.mif -coord 3 0 -stride 1,2,3,4 5tt-gm.nii.gz                                                                                                                                                                          
flirt -in mean_b0_preproc.nii.gz -ref 5tt-gm.nii.gz -dof 6 -omat diff2struct_fsl.mat                                                                                                                                                   
transformconvert diff2struct_fsl.mat mean_b0_preproc.nii.gz 5tt-gm.nii.gz flirt_import diff2struct_mrtrix.txt
...

I’m pretty sure I’ve seen other approaches mentioned on the forum, I recommend you search for them and see what works best.

[Alex_Sphyrna]

It worked excellent.
Thanks!