From 4eaf84a1a538edd14db6101321e5e0c87a577e30 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Tue, 26 Oct 2021 21:37:10 +0200 Subject: [PATCH] enh: expand pepolar and alternatives --- docs/methods.rst | 33 ++++++++++++++++++++++++++++----- 1 file changed, 28 insertions(+), 5 deletions(-) diff --git a/docs/methods.rst b/docs/methods.rst index 2d5ccba088..e0e59f64f1 100644 --- a/docs/methods.rst +++ b/docs/methods.rst @@ -103,6 +103,11 @@ already been calculated (see `the corresponding section of BIDS :abbr:`PEPOLAR (Phase Encoding POLARity)` techniques ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Alternatively, it is possible to estimate the field by exploiting the symmetry of the +distortion when the PE polarity is reversed. +*SDCFlows* integrates two implementations based on FSL ``topup`` [Andersson2003]_, +and AFNI ``3dQwarp`` [Cox1997]_. + This corresponds to `this section of the BIDS specification `__. @@ -152,12 +157,18 @@ EPI given as input into its *unwarped* mapping. The estimated transform is then converted into a :math:`B_0` fieldmap in Hz, which can be stored within the derivatives folder. -.. danger :: Experimental feature +.. danger :: This procedure is experimental, and the outcomes should be scrutinized one-by-one and used with caution. Feedback will be enthusiastically received. +Other (unsupported) approaches +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +There exist some alternative options to estimate the fieldmap, such as mapping the +point-spread-function [Zaitsev2004]_, or by means of nonlinear registration of brain +surfaces onto the distorted :abbr:`EPI (echo-planar imaging)` data [Esteban2016]_. + Estimation tooling ~~~~~~~~~~~~~~~~~~ The workflows provided by :py:mod:`sdcflows.fit` make use of several utilities. @@ -209,15 +220,21 @@ It is possible to force the fieldmap-less estimation by passing ``force_fmapless References ---------- -.. [Jezzard1995] Jezzard, P. & Balaban, R. S. Correction for geometric distortion in - echo planar images from B0 field variations. Magn. Reson. Med. 34:65–73, 1995 +.. [Jezzard1995] Jezzard, P. & Balaban, R. S. (1995) Correction for geometric distortion in + echo planar images from B0 field variations. Magn. Reson. Med. 34:65–73. doi:`10.1002/mrm.1910340111 `__. -.. [Hutton2002] Hutton et al., Image Distortion Correction in fMRI: A Quantitative - Evaluation, NeuroImage 16(1):217-240, 2002. doi:`10.1006/nimg.2001.1054 +.. [Hutton2002] Hutton et al., (2002) Image Distortion Correction in fMRI: A Quantitative + Evaluation, NeuroImage 16(1):217-240. doi:`10.1006/nimg.2001.1054 `__. .. [Jenkinson2003] Jenkinson, M. (2003) Fast, automated, N-dimensional phase-unwrapping algorithm. MRM 49(1):193-197. doi:`10.1002/mrm.10354 `__. +.. [Andersson2003] Andersson, J. (2003) How to correct susceptibility distortions in spin-echo + echo-planar images: application to diffusion tensor imaging. NeuroImage 20:870–888. + doi:`10.1016/s1053-8119(03)00336-7 `__. +.. [Cox1997] Cox, R. (1997) Software tools for analysis and visualization of fMRI data. NMR Biomed. + 10:171–178, doi:`10.1002/(sici)1099-1492(199706/08)10:4/5%3C171::aid-nbm453%3E3.0.co;2-l + `__. .. [Studholme2000] Studholme et al. (2000) Accurate alignment of functional EPI data to anatomical MRI using a physics-based distortion model, IEEE Trans Med Imag 19(11):1115-1127, 2000, doi: `10.1109/42.896788 @@ -235,3 +252,9 @@ References Coregistration of BOLD EPI and T1w Images `__, Berlin: Master Thesis, Freie Universität. +.. [Zaitsev2004] Zaitsev, M. (2004) Point spread function mapping with parallel imaging techniques and + high acceleration factors: Fast, robust, and flexible method for echo-planar imaging distortion correction, + MRM 52(5):1156-1166. doi:`10.1002/mrm.20261 `__. +.. [Esteban2016] Esteban, O. (2016) Surface-driven registration method for the structure-informed segmentation + of diffusion MR images. NeuroImage 139:450-461. + doi:`10.1016/j.neuroimage.2016.05.011 `__.