VOI's in FSL space

MNI VOI's can be converted for tracking in FSL. There are three steps:

1. Convert VOI to native T1 space
2. Warp to DTI space
3. Reslice into FSL-compatible nifti file

1. Convert VOI to native T1 space

Use the DARTEL Created Inverse Warped option

• Select the flow fields from the T1 reference (...\T1preprocess\Study_999\T1_ref_vox...\u_*.nii)
• Select the images (VOI in MNI space)
• Run with the defaults.

This creates native-space VOI in the T1 folder, prepended with "w" and with suffix of the deformation field

Example:  "Left Hippocampus.nii" written as "wLeft Hippocampus_u_rc1rE9560101112017S02-0001.nii"

2. Warp to DTI space

Use the old spatial normalization (pre DARTEL) to warp from T1 to DTI space.

• Create a new subject, select the ..._seg_inv_sn.mat from the DTI preprocess folder
  • These files are in the "b0_images" subfolder. (e.g., ...\DTIpreprocess\NP\Subject_956_RightPain\DTIE9560101112017S4\dw_raw\b0_images)
• Select the images created above
• In the writing options, for best accuracy change the voxel sizes to \[1 1 1]
• For clarity, change the prefix to dti