TBSS (FSL) implementation with ANTs and T1w registration to template. ants_tbss creates the TBSS skeleton using ANTS without FA to FA registrations.
There are essentially two steps: (a) Inter-modality, intrasubject registration of the B0 image to subject T1w image (b) Registration of subject T1w image the MNI152 1mm brain template (by default).
The software requires tight brain extractions for the T1w images. Brain extraction using antsBrainExtraction.sh and based on recommended settings from fMRIprep.
It is also possible to use ants_tbss (--othermodality) for registration of other modalities such as fMRI (e.g., betted example_func.nii.gz) to B0-in-native-T1w, and use the previously calculated transformations to native space and standard space.
voxel_slices is also installed for fast production of quality controls images.
e.g.,
Autothresholded FA on T1w image in MNI_1mm space
FA with MNI_1mm brain image auththresholded segmentation
Skeletonized FA on mean FA in MNI_1mm space
Citation: Tustison NJ, Avants BB, Cook PA, Kim J, Whyte J, Gee JC, Stone JR. Logical circularity in voxel-based analysis: normalization strategy may induce statistical bias. Hum Brain Mapp. 2014 Mar;35(3):745-59. doi: 10.1002/hbm.22211.
Also read this post from the ANTS forum: https://sourceforge.net/p/advants/discussion/840261/thread/e6fc9a8c/
If you use the ants brain extraction script:
The script antsBrainExtraction.sh was used to perform brain extraction including N4BiasFieldCorrection and the OASIS template.
Tustison NJ, Avants BB, Cook PA, Zheng Y, Egan A, Yushkevich PA, Gee JC. N4ITK: improved N3 bias correction. IEEE Trans Med Imaging. 2010 Jun;29(6):1310–20. doi:10.1109/TMI.2010.2046908.
virtualenv -p python3.7 python37env
source python37env/bin/activate
pip install git+https://github.com/trislett/ants_tbss.git
Make a text file with betted B0 images
for i in $(cat subjects); do echo /path/to/images/${i}*B0*nii.gz; done > B0_brain_list
Make a text file with betted T1w images
for i in $(cat subjects); do echo /path/to/images/${i}*T1w_T1_BrainExtractionBrain.nii.gz; done > T1w_brain_list
Make a text file with betted B0 images
for i in $(cat subjects); do echo /path/to/images/${i}*FA*nii.gz; done > FA_list
Run ants_tbss
ants_tbss --antsregtotemplate B0_brain_list T1w_brain_list --runtbss FA_list FA -nlws --numthreads 8