HELP: ANTs registration + transformation = outcome incorrectly registered image

[didatto]

Hi,
I am running a DTI analyis in FSL, but trying to use ANTs for better registration.
I am mainly focusing on the precuneus.
I run the registration with the following code, however the image I received was not quite the precuneus.

The precuneus mask was used from the FSL's built in Harvard- Oxford Atlas.
Can somebody assist me in the problem? Did I mix up the images at one of the registration steps?
This is my code:

##00.0 ANTs-PATH 
export PATH=/opt/ants/bin:$PATH 
##00.1 defining & creating a folder
mkdir -p /Volumes/Diana/Preprocessed/DTI/Test_BedpostX/ANTs/T1_MNI
T1_folder="/Volumes/Diana/Preprocessed/DTI/Test_BedpostX/ANTs/T1_MNI"


##01.1 defining the path #to t1brain 
template="/Users/anneliesvantwesteinde/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz"
t1brain="/Volumes/Diana/Preprocessed/DTI/Test_BedpostX/ADDI_013/ADDI_013_T1/ADDI_013_T1.nii"
#01.2 Registration Atlas T1 - > subject T1 (non-linear):
antsRegistration -d 3 --float 0 --output "$T1_folder"/out \
--interpolation Linear \
--winsorize-image-intensities [0.005,0.995] \
--use-histogram-matching 0 \
--initial-moving-transform [$template,$t1brain,1] \
--transform Rigid[0.1] \
--metric MI[$template,$t1brain,1,32,Regular,0.25] \
--convergence [1000x500x250x100,1e-6,10] \
--shrink-factors 8x4x2x1 \
--smoothing-sigmas 3x2x1x0vox \
--transform Affine[0.1] \
--metric MI[$template,$t1brain,1,32,Regular,0.25] \
--convergence [1000x500x250x100,1e-6,10] \
--shrink-factors 8x4x2x1 \
--smoothing-sigmas 3x2x1x0vox \
--transform SyN[0.1,3,0] \
--metric CC[$template,$t1brain,1,4] \
--convergence [100x70x50x20,1e-6,10] \
--shrink-factors 8x4x2x1 \
--smoothing-sigmas 3x2x1x0vox \
    --verbose 1

##02.1 defining the path
b0brain="/Volumes/Diana/Preprocessed/DTI/Addison_AllControls/ADDI_013/nodif.nii.gz" 
t1brain_mask="/Volumes/Diana/Preprocessed/T1/BrainMasks/FSL_Anat_Addison_AllControls/ADDI_013_T1/ADDI_013_T1.anat/T1_biascorr_brain_mask.nii.gz"
#02.2creating a separate folder 
mkdir -p "$T1_folder"/b0_T1
#02.3 Registration Subject b0 -> Subject T1 (linear/affine):
antsRegistrationSyN.sh -d 3 -f "$t1brain" -m "$b0brain" -o "$T1_folder/b0_T1/out" -n 4 -t a -x "$t1brain_mask"
 
##03.1 defining the path, creating another folder  
ROI_mask="/Users/anneliesvantwesteinde/precuneus/precuneus_ROI_Left.nii.gz"
new_mask_dir="$T1_folder/"
mkdir -p "$T1_folder"/new_mask_dir
filename_mask=$(basename "$ROI_mask" .nii.gz)
#03.2 Then we bring the ROI from Atlas T1 -> subject T1 -> subject b0 
antsApplyTransforms -d 3 -i "$ROI_mask" -r $b0brain -t ["$T1_folder"/b0_T1/out0GenericAffine.mat,1] -t ["$T1_folder"/out0GenericAffine.mat,1] -t "$T1_folder"/out1InverseWarp.nii.gz -n NearestNeighbor -o "$T1_folder/new_mask_dir/${filename_mask}_in_T2.nii.gz" -v

#04.01 defining
DWI_folder="/Volumes/Diana/Preprocessed/DTI/Test_BedpostX/ADDI_013.bedpostX"
directory_path="$DWI_folder/probtrackx"
mkdir -p "$directory_path"

#04. give exact path! "$filename_mask"_in_T2.nii.gz is the file you will supply to the probtrackx2. For example, like this:
probtrackx2 \
    -x "/Volumes/Diana/Preprocessed/DTI/Test_BedpostX/ANTs/T1_MNI/new_mask_dir/precuneus_ROI_Left_in_T2.nii.gz" \
    -V 1 \
    -l \
    --modeuler \
    --onewaycondition -c 0.2 -S 2000 \
    --steplength=0.5 \
    -P 5000 \
    --fibthresh=0.01 \
    --distthresh=0.0 \
    --sampvox=0.0 \
    --forcedir \
    --opd \
    -s "$DWI_folder"/merged \
    -m "$DWI_folder"/nodif_brain_mask.nii.gz \
    --dir="$directory_path" 

I am using bash for running this script and my operating system and version macOS-14.0; CPU architecture arm64 (Apple M1/M2)

The outcome of the probtrackx - the fdt_paths.nii.gz in fsleyes:

Thank you for your help in advance!