Outputs to PreFreeSurfer

The purpose

1. To average image repeats # PanLab does not use this step, since we only acquire one set of structurals
2. To create a native, undistored strucutral volume space for the subject. Which means
   • Distortion corrected for the gradient (scanner-specific, vednor-designed distoriton) and B0 distortions (fieldmap distortion) # We do not do Gradient Distortion Corection
   • Rigidly realign to the axes of MNI space (but does not warp to MNI)
3. Robust brain extraction
4. Aligns T1 and T2
5. Bias field correction
   • Calculated from the square root of the product of the T1 and T2
6. Warp to MNI

• Uses fnirt

Makes the following folders and files:

1. T1w * ACPCAlignment
   1. robustroi.nii.gz # is the T1 without the neck and lower head
   2. T1w_acpc.nii.gz # Resamples (if using a higher res template) and uses applywarp to linearly transform to MNI152 using output of acpc_final and a 6DOF approximation
   3. acpc_final.nii.gz # flirt used with cropped image 12DOF to linearly transform to MNI152 * BrainExtraction_FNIRTbased
   4. T1w_acpc_brain_mask # fslmaths to apply mni mask to T1_acpc (which is not nonlinearly-warped)
   5. T1w_acpc_to_MNI_roughlin.nii.gz # gets a first rough estimate of the linearly warp using 2mm template
   6. T1w_acpc_to_MNI_nonlin.nii.gz # warping rough linear and nonlinear image to the high res template * xfms Transformation matrices and warp fields * BiasFieldCorrection_sqrtT1wXT1w
   7. T1w_acpc_dc_brain.nii.gz # suffix of "_dc" indicates distortion corection. since we do not do distortion correction, T1w_acpc and T1w_acpc_dc are equivalent
   8. T1w_acpc_dc_restore.nii.gz # T1w_acpc image corrected by the bias_field image
   9. bias_raw.nii.gz # take the normalized sqrt image (but not smoothed image), mask out the csf and "extrapolate" to the entire FOV
   10. T1wmultT2w_brain_norm_s5.nii.gz # T1wmultT2w_brain_norm.nii.gz smoothed by a bias field smoothing sigma (in our case 5)
   11. T1wmultT2w_brain_norm.nii.gz # Literally sqrt(|T1w * T2w|)/mean(sqrt(|T1w * T2w|)) (our guess of bias field correction)
2. T2w * ACPCAlignment
   1. robustroi.nii.gz #
   2. T2w_acpc.nii.gz #
   3. acpc_final.nii.gz # * BrainExtraction_FNIRTbased
   4. T2w_acpc_brain_mask #
   5. T2w_acpc_to_MNI_roughlin.nii.gz #
   6. T2w_acpc_to_MNI_nonlin.nii.gz # * xfms Transformation matrices and warp fields *T2wToT1wDistortionCorrectAndReg
   7. Unknown must learn #
3. MNINonLinear * xfms Transformation matrices and warp fields