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 (example job file on right).

• 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 (example job file on right).

• 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.

This will create files prepended with "dti".

3. Reslice into FSL-compatible format

To be read in FSL, the file needs to be the same orientation and voxel size as the image being masked, and there must be no spaces in the file name. There is a custom command in CSPM Image menu

• Select the reference image to slice
• Select the VOI