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ANTS TBSS

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trislett edited this page Oct 5, 2019 · 12 revisions

ants_tbss is released! Please go here: https://github.com/trislett/ants_tbss

THIS PAGE IS OBSOLETE. A NEW VERSION OF SCRIPTS WILL BE RELEASED SOON! (See above!)

Creation of the TBSS skeleton using ANTS. There are essentially two steps: (a) Inter-modality, intrasubject registration of the DWI image to subject T1w image (b) Non-linear registration of subject T1w image the MNI152 1mm brain template

These steps assume that $TFCE_mediation variable has been exported to the environment.

E.g.,

export TFCE_mediation=/path/to/tfce_mediation/clone/directory

  • Read/cite: 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.

  • Read this post from the ANTS forum: https://sourceforge.net/p/advants/discussion/840261/thread/e6fc9a8c/

  1. Output subjects names to test file (one per line)
for i in *_FA.nii.gz; do echo $(basename $i _FA.nii.gz); done > subjects;
mkdir FAimages; mkdir T1images
  1. Move FA images to folder
mv *_FA.nii.gz FAimages/
  1. convert normalized freesurfer t1 weighted image to nifti, rename, and copy to T1_images. The subjects must match what's in the freesurfer $SUBJECTS_DIR.
for i in $(cat subjects); do 
   echo mri_convert $SUBJECTS_DIR/${i}/mri/brainmask.mgz T1images/${i}_T1_brain.nii.gz --out_orientation RAS; 
done | parallel -j 8
  1. echo nl_FAtoStd.sh for all subjects (FA to T1 using MI; T1 to Standard image using SyN)
for i in $(cat subjects); do 
   echo $TFCE_mediation/tfce_mediation/misc_scripts/nl_FAtoStd.sh ${PWD}/FAimages/${i}*FA*z ${PWD}/T1images/${i}*T1*z ${FSLDIR}/data/standard/MNI152_T1_1mm_brain.nii.gz; 
done > cmd_FAtoStd
  1. Use your favourite tool for parallelization (htcondor used here). Note, this step will use a lot of disk space.
$TFCE_mediation/tfce_mediation/tools/submit_condor_jobs_file cmd_FAtoStd
  1. Create FA skeleton
$TFCE_mediation/tfce_mediation/misc_scripts/create_skeleton.sh -t 0.2 -m -s
  1. Run statistics using TFCE_mediation or randomise.

Note, ANTS binaries and scripts, as well the FSL binaries must be in your PATH. If not, add them to your bashrc, or edit the bash scripts accordingly (i.e., in nl_FAtoStd.sh, and in create_skeleton.sh)

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