Hello Mrtrix3rs,
I’m trying to register the glasser + aseg atlas to diffusion data. Ideally, I would rather use bbregister than flirt. As the transform mats are not identical between the two methods, which one is recommended? Is there any way I could still use the dwi2orig.dat and perform some operation on it to get it to what mrtrix “expects”?
Method 1: Register atlas using bbregister.
bbregister --s sub-i --mov b0_preproc.nii.gz --reg dwi2orig.dat --t2 --init-fsl
mri_vol2vol --s sub-i --mov b0_preproc.nii.gz --reg dwi2orig.dat --targ glasser+aseg.nii.gz --o glasser+aseginDWI.nii.gz --inv --interp nearest
transformconvert dwi2orig.dat b0_preproc.nii.gz orig.mgz flirt_import dwi2orig_mrtrix.txt -force
mrconvert glasser+aseg.nii.gz glasser+aseg_good.mif -force
mrtransform glasser+aseg.mif -linear dwi2orig_mrtrix.txt glasser_aseg_parcels_coreg_dwi2orig_mrtrix.mif –inverse
Method 2: Register atlas using flirt.
flirt -in b0_preproc.nii.gz -ref T1_raw.nii.gz -interp nearestneighbour -dof 6 -omat dwi2T1_fsl.mat
transformconvert dwi2T1_fsl.mat b0_preproc.nii.gz T1_raw.nii.gz flirt_import dwi2T1_mrtrix.txt -force
mrconvert glasser+aseg.nii.gz glasser+aseg_good.mif -force
mrtransform glasser+aseg_good.mif -interp nearest -linear dwi2T1_mrtrix.txt –inverse glasser_aseg_parcels_coreg.mif -force
__Error:__ Note i'm getting the following error when using mrtransform.
mrtransform: [ERROR] Expected exactly 2 arguments (3 supplied)
mrtransform: [ERROR] Usage: mrtransform input output
mrtransform: [ERROR] Yours: mrtransform glasser+aseg.mif –inverse glasser_aseg_parcels_coreg.mif
Many thanks for any help you can offer!
-Heena