ROI-based fixel-based analysis

[hyting]

Hi, @NicDC
Many thank you for your reply.

Follow your suggestion

@NicDC

The BNA is already in MNI152 space as far as I can tell, so you shouldn’t need to register it again

@NicDC

Don’t use nearest neighbor interpolation while calculating the transform and warp, only when applying it to move the label image (atlas) to the wmfod_template

I have upgraded my code as followed, and it works perfectly!!

flirt -ref ../MNI152_T1_1mm_brain.nii.gz -in I0image.nii.gz -omat template2mni.mat -dof 12

fnirt --ref=../MNI152_T1_1mm_brain.nii.gz --in=I0image.nii.gz --aff=template2mni.mat --cout=warps_template2mni

invwarp --ref=I0image.nii.gz --warp=warps_template2mni --out=warps_mni2template

warpinit ../MNI152_T1_1mm_brain.nii.gz inv_identity_warp_no_mni.nii

applywarp --ref=I0image.nii.gz --in=inv_identity_warp_no_mni.nii --warp=warps_mni2template.nii.gz --out=mrtrix_warp_mni2template.nii.gz

mrtransform ../BN_Atlas_246_1mm.nii.gz -warp mrtrix_warp_mni2template.nii.gz bna246toTemplate_mni.nii.gz -template wmfod_template.mif -interp nearest

mrconvert bna246toTemplate_mni.nii.gz bna246toTemplate_mni.mif

And given the thread you quoted, I’ve tried exactly as what the @maxpietsch suggested, and worked successfully, but the results were even weirder . After applying the warp to the Atlas, some labels disappeared. I have found that some regions disappeared in the warp_MNI152.mif, but I’m not familiar with ANTs, so I have no idea how to optimize it, would you please guide me?

## warp image use ANTs nonlinear
#transform the template_mask.mif to the ANTs compatible format
mrconvert template_mask.mif template_mask.nii.gz

# register MNI152 to the I0image 
antsRegistration --verbose 1 --dimensionality 3 --float 0 --output [ants,antsWarped.nii.gz,antsInverseWarped.nii.gz] --interpolation Linear --use-histogram-matching 1 --winsorize-image-intensities [0.005,0.995] --transform Rigid[0.1] --metric CC[I0image.nii.gz,../MNI152_T1_1mm_brain.nii.gz,1,4,Regular,0.1] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform Affine[0.1] --metric CC[I0image.nii.gz,../MNI152_T1_1mm_brain.nii.gz,1,4,Regular,0.2] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform SyN[0.1,3,0] --metric CC[I0image.nii.gz,../MNI152_T1_1mm_brain.nii.gz,1,4] --convergence [100x70x50x20,1e-6,10] --shrink-factors 4x2x2x1 --smoothing-sigmas 2x2x1x0vox -x [template_mask.nii.gz,../MNI152_T1_1mm_brain_mask.nii.gz]

# Generate an identity (deformation field) warp
warpinit ../MNI152_T1_1mm_brain.nii.gz identity_warp[].nii

# Transform this identity warp
for i in {0..2}; do
    antsApplyTransforms -d 3 -e 0 -i identity_warp${i}.nii -o mrtrix_warp${i}.nii -r I0image.nii.gz -t ants1Warp.nii.gz -t ants0GenericAffine.mat --default-value 2147483647
done

# Correct the warp
warpcorrect mrtrix_warp[].nii mrtrix_warp_corrected.mif -marker 2147483647

# Warp the image
mrtransform ../MNI152_T1_1mm_brain.nii.gz -warp mrtrix_warp_corrected.mif warped_MNI152.mif

# check that the conversion went as expected by comparison with ANTs’ output
mrview warped_MNI152.mif -overlay.load antsWarped.nii.gz -overlay.opacity 0.3

# Apply the warp to Atlas (with regridding)
mrtransform ../BN_Atlas_246_1mm.nii.gz -warp mrtrix_warp_corrected.mif -interp nearest BN_Atlas_246_1mm_to_wmfodtemplate.mif

# Check everything worked
mrview wmfod_template.mif -roi.load BN_Atlas_246_1mm_to_wmfodtemplate.mif -roi.opacity 0.3

@NicDC

I was giving you instructions on how to move the Atlas labels to the wmfod_template so that you could use the labels to build a connectome (using tck2connectome) and then select the tracks assigned to the thalamus nodes (using connectome2tck).

@NicDC

Depends on what you want to do - I was giving you instructions on how to move the Atlas labels to the wmfod_template so that you could use the labels to build a connectome (using tck2connectome) and then select the tracks assigned to the thalamus nodes (using connectome2tck). I think this is what the authors of that paper did, but you could also approach it by warping the tracks to MNI space and then doing something similar - not sure whether one approach is better than the other.

Sorry, I got a bit confused. Is there any difference between the registration results reults form the ANTs and the FSL? They seem the same when overlaying the results (i.e. Atlas2wmfod_template.mif) with the wmfod_template, ideally. So I can also using tck2connectome and connectome2tck with the warped results (i.e. Atlas2wmfod_template.mif) which I generated from FSL, right?

Sorry for the lengthy questions, and thank you very much for your patience and kindness.

Best wishes,
Yuting.