extract_FA

Software

• ANTS (2.1.0-gGIT-N)
• fsl (5.0.9; eddy: eddy-patch-fsl-5.0.11)
• mrtrix3 (3.0.1)
• nipype (1.5.1)
• nilearn (0.6.2)

Pipeline

Preprocessing

• mrtrix denoise

  Veraart, J.; Novikov, D.S.; Christiaens, D.; Ades-aron, B.; Sijbers, J. & Fieremans, E. Denoising of diffusion MRI using random matrix theory. NeuroImage, 2016, 142, 394-406, doi: 10.1016/j.neuroimage.2016.08.016

  Veraart, J.; Fieremans, E. & Novikov, D.S. Diffusion MRI noise mapping using random matrix theory. Magn. Res. Med., 2016, 76(5), 1582-1593, doi: 10.1002/mrm.26059

• fsl eddy (with repol option)

  The main reference that should be cited when using eddy is Jesper L. R. Andersson and Stamatios N. Sotiropoulos. An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. NeuroImage, 125:1063-1078, 2016.

  If you use the --repol (replace outliers) option, please also reference Jesper L. R. Andersson, Mark S. Graham, Eniko Zsoldos and Stamatios N. Sotiropoulos. Incorporating outlier detection and replacement into a non-parametric framework for movement and distortion correction of diffusion MR images. NeuroImage, 141:556-572, 2016.

• Dwibiascorrect (with ANTS)

  If using -ants option: Tustison, N.; Avants, B.; Cook, P.; Zheng, Y.; Egan, A.; Yushkevich, P. & Gee, J. N4ITK: Improved N3 Bias Correction. IEEE Transactions on Medical Imaging, 2010, 29, 1310-1320

• Mask

  • Dwi2mask for lhab Dhollander T, Raffelt D, Connelly A. Unsupervised 3-tissue response function estimation from single-shell or multi-shell diffusion MR data without a co-registered T1 image. ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 2016, 5.

  • FSL's BET for camcan, as this produced better results

Tensor fit

• Dwi2tensor

  Veraart, J.; Sijbers, J.; Sunaert, S.; Leemans, A. & Jeurissen, B. Weighted linear least squares estimation of diffusion MRI parameters: strengths, limitations, and pitfalls. NeuroImage, 2013, 81, 335-346

• Tensor2metric

  Basser, P. J.; Mattiello, J. & Lebihan, D. MR diffusion tensor spectroscopy and imaging. Biophysical Journal, 1994, 66, 259-267

  Westin, C. F.; Peled, S.; Gudbjartsson, H.; Kikinis, R. & Jolesz, F. A. Geometrical diffusion measures for MRI from tensor basis analysis. Proc Intl Soc Mag Reson Med, 1997, 5, 1742

MNI

• AntsRegistrationSyn

  http://www.ncbi.nlm.nih.gov/pubmed/20851191

  http://www.frontiersin.org/Journal/10.3389/fninf.2013.00039/abstract

  Normalization to JHU-ICBM-FA-1mm.nii.gz

extract metrics

masked metrics with thresholded FA >.2 mask. Extracted mean values from ROIs defined in JHU/JHU-ICBM-tracts-maxprob-thr{25, 50}-1mm.nii.gz (distributed with FSL). Extraction with nilearn.NiftiLabelsMasker.

Changes

• v2.1 initial
• v2.2 fixed raise if processing fails
• v3 camcan: fsl bet for mask
• v4 version updates and olm ready
• v4.fix fixes an issue with writing the same plot multiple times