# NL REG TESTS

# TEST 1: NL reg only T1-registered T2 to MNI and apply warp to both T1 and T2
**STEP 1: register cropped T1 to cropped T2**

**STEP 2: NL register T1-registered T2 to T2 MNI template**

**STEP 3: convert following files to ants warps:**
`resized/xfms/cropT2tocropT1.mat`
`resized/ACPC_align/T1w_full2crop.mat`
`resized/ACPC_align/T2w_full2crop.mat`

**STEP 4: T1 apply affine and T2 warps**
`WarpImageMultiTransform 3 averaged/sub-*_0000.nii.gz preBIBSnet_final_0000.nii.gz -R INFANT_MNI_T2_1mm.nii.gz T1w_full2crop_ants.txt T2/antsregWarp.nii.gz T2/antsregAffine.txt`

**STEP 5: T2 apply warps**
`WarpImageMultiTransform 3 averaged/sub-*_0001.nii.gz preBIBSnet_final_0001.nii.gz -R INFANT_MNI_T2_1mm.nii.gz T2w_full2crop_ants.txt cropT2tocropT1_ants.txt T2/antsregWarp.nii.gz T2/antsregAffine.txt`

**Results: good registration and no holes for 1022, but 1025 still has holes**

# TEST 2: NL reg both T1 & T1-registered T2 to respective MNI atlases
**STEP 1: register cropped T1 to cropped T2**

**STEP 2: NL register crop T1 and T1-reg T2 to MNI templates**

**STEP 3: convert following files to ants warps:**
`resized/xfms/cropT2tocropT1.mat`
`resized/ACPC_align/T1w_full2crop.mat`
`resized/ACPC_align/T2w_full2crop.mat`

**STEP 4: T1 apply warps**
`WarpImageMultiTransform 3 averaged/sub-*_0000.nii.gz preBIBSnet_final_0000.nii.gz -R INFANT_MNI_T1_1mm.nii.gz T1w_full2crop_ants.txt T1/antsregWarp.nii.gz T1/antsregAffine.txt`

**STEP 5: T2 apply warps**
`WarpImageMultiTransform 3 averaged/sub-*_0001.nii.gz preBIBSnet_final_0001.nii.gz -R INFANT_MNI_T2_1mm.nii.gz T2w_full2crop_ants.txt cropT2tocropT1_ants.txt T2/antsregWarp.nii.gz T2/antsregAffine.txt`

**Results: aseg is partially cut off. final T1/2 registration somewhat poor after nonlinear reg even though inputs are well-registered**

# TEST 3: NL register crop T1 and crop T2 separately to respctive templates, then register NL-reg T2 to NL-reg T1 after

**STEP 1: Perform nonlinear registration of cropped T1 and cropped T2 to respective MNI atlases in separate working directories**
`ANTS 3 -m CC[INFANT_MNI_T<1/2>_1mm.nii.gz,cropped/T1w/sub-*_000<0/1>.nii.gz,1,5] -t SyN[0.25] -r Gauss[3,0] -o antsreg -i 60x50x20 --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 --MI-option 32x16000`

**STEP 1 TEMP: Apply nonlinear warps to cropped T1/T2 just as sanity check for debugging**
`antsApplyTransforms -d 3 --output T<1/2>w_NL_reg.nii.gz --reference-image INFANT_MNI_T<1/2>_1mm.nii.gz --transform antsregWarp.nii.gz antsregAffine.txt --input cropped/T1w/sub-*_000<0/1>.nii.gz --interpolation BSpline`

**STEP 2: Invert crop matrices**
`convert_xfm -inverse cropped/T<1/2>w/crop2full.mat -omat resized/ACPC_align/T<1/2>w_full2crop.mat`

**STEP 3: Convert T<1/2>w_full2crop.mat to ANTS warps**
`c3d_affine_tool -ref cropped/T1w/sub-*_000<0/1>.nii.gz -src averaged/sub-*_000<0/1>.nii.gz T<1/2>w_full2crop.mat -fsl2ras -oitk T<1/2>w_full2crop_ants.txt`

**STEP 4: Apply T<1/2>w_full2crop.mat and NL reg warps to average anatomicals**
`WarpImageMultiTransform 3 averaged/sub-*_0000.nii.gz T1w_NL_reg.nii.gz -R INFANT_MNI_T1_1mm.nii.gz T1w_full2crop_ants.txt T1/antsregWarp.nii.gz T1/antsregAffine.txt`

`WarpImageMultiTransform 3 averaged/sub-*_0001.nii.gz T2w_NL_reg.nii.gz -R INFANT_MNI_T2_1mm.nii.gz T2w_full2crop_ants.txt T2/antsregWarp.nii.gz T2/antsregAffine.txt`

**STEP 5: Register NL-registered T2 to NL-registered T1**
`flirt -ref T1w_NL_reg.nii.gz -in T2w_NL_reg.nii.gz -omat nlcropT2tonlcropT1.mat -out NL_T2w_registered_to_T1w.nii.gz -cost mutualinfo -searchrx -15 15 -searchry -15 15 -searchrz -15 15 -dof 6`

**STEP 6: Convert nlcropT2tonlcropT1.mat to ANTS warp**
`c3d_affine_tool -ref T1w_NL_reg.nii.gz -src T2w_NL_reg.nii.gz nlcropT2tonlcropT1.mat -fsl2ras -oitk nlcropT2tonlcropT1_ants.txt`

**STEP 7: Apply full2crop, NL registration, and nl T2-to-T2 registration warps to average T2**
`WarpImageMultiTransform 3 averaged/sub-*_0001.nii.gz preBIBSnet_final_0001.nii.gz -R INFANT_MNI_T2_1mm.nii.gz T2w_full2crop_ants.txt T2/antsregWarp.nii.gz T2/antsregAffine.txt nlcropT2tonlcropT1_ants.txt`