I am running Mac OS BigSur 11.2.3 on Intel i9 8-core 2.4 GHz, 64GB memory. I have installed both MRTrix3 and MRTrix 3Tissue, but only MRtrix3 is exported to my $PATH.
I am trying to register a subject’s T1 scan to their diffusion scan with the following commands:
flirt -in $DIFFUSION -ref $T1 -dof 6 -cost normmi -omat dwi2T1.mat -out dwi2T1.nii convert_xfm -inverse -omat T12dwi.mat dwi2T1.mat transformconvert dwi2T1.mat $DIFFUSION $T1 flirt_import dwi2T1_mrtrix.txt -force mrtransform $t1 -linear dwi2T1_mrtrix.txt -inverse T12dwi.nii -force
The problem is that my final output T12dwi.nii image contains missing slices intermittently when I run the above commands. No error is thrown and it can work but if I run the same commands again- the displayed image shows a slice or 2 missing- see attached image.
I am unsure why this is and it does not seem to be rendering issue as this is seen in mrview and fslview. I know that my input T1 and DIFFUSION scan are fine- see attached. I also know that dwi2T1.nii from the flirt output is also fine- see attached.
The diffusion scan has been preprocessed:
mrdenoise → mrdegibb → fsl TOPUUP (TOPUP was run after synb0 as I only have 1 b0: GitHub - MASILab/Synb0-DISCO) → fsl EDDY → dwibiascorrect → mrconvert -coord 3 0 -axes 0,1,2 to extract b0 image (I only have 1 b0 image).
Has anyone encountered this before?