Scripts for external libraries¶
5ttgen¶
Synopsis¶
5ttgen [ options ]
Description¶
Generate a 5TT image suitable for ACT
Standard options¶
- -continue <TempDir> <LastFile> Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file
- -force Force overwrite of output files if pre-existing
- -help Display help information for the script
- -nocleanup Do not delete temporary directory at script completion
- -nthreads number Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)
- -tempdir /path/to/tmp/ Manually specify the path in which to generate the temporary directory
- -quiet Suppress all console output during script execution
- -verbose Display additional information for every command invoked
References¶
ACT: Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information. NeuroImage, 2012, 62, 1924-1938
bet: Smith, S. M. Fast robust automated brain extraction. Human Brain Mapping, 2002, 17, 143-155
fast: Zhang, Y.; Brady, M. & Smith, S. Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm. IEEE Transactions on Medical Imaging, 2001, 20, 45-57
first: Patenaude, B.; Smith, S. M.; Kennedy, D. N. & Jenkinson, M. A Bayesian model of shape and appearance for subcortical brain segmentation. NeuroImage, 2011, 56, 907-922
FSL: Smith, S. M.; Jenkinson, M.; Woolrich, M. W.; Beckmann, C. F.; Behrens, T. E.; Johansen-Berg, H.; Bannister, P. R.; De Luca, M.; Drobnjak, I.; Flitney, D. E.; Niazy, R. K.; Saunders, J.; Vickers, J.; Zhang, Y.; De Stefano, N.; Brady, J. M. & Matthews, P. M. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 2004, 23, S208-S219
—
Author: Robert E. Smith (robert.smith@florey.edu.au)
Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors
This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/
MRtrix is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see www.mrtrix.org
dwi2response¶
Synopsis¶
dwi2response [ options ]
Description¶
Estimate response function(s) for spherical deconvolution
Standard options¶
- -continue <TempDir> <LastFile> Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file
- -force Force overwrite of output files if pre-existing
- -help Display help information for the script
- -nocleanup Do not delete temporary directory at script completion
- -nthreads number Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)
- -tempdir /path/to/tmp/ Manually specify the path in which to generate the temporary directory
- -quiet Suppress all console output during script execution
- -verbose Display additional information for every command invoked
References¶
MSMT_CSD: Jeurissen, B.; Tournier, J.-D.; Dhollander, T.; Connelly, A. & Sijbers, J. Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data. NeuroImage, 2014, 103, 411-426
SD: Tournier, J.-D.; Calamante, F.; Gadian, D. G. & Connelly, A. Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution. NeuroImage, 2004, 23, 1176-1185
Tax2014: Tax, C. M.; Jeurissen, B.; Vos, S. B.; Viergever, M. A. & Leemans, A. Recursive calibration of the fiber response function for spherical deconvolution of diffusion MRI data. NeuroImage, 2014, 86, 67-80
Tournier2013: Tournier, J.-D.; Calamante, F. & Connelly, A. Determination of the appropriate b value and number of gradient directions for high-angular-resolution diffusion-weighted imaging. NMR Biomedicine, 2013, 26, 1775-1786
—
Author: Robert E. Smith (robert.smith@florey.edu.au)
Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors
This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/
MRtrix is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see www.mrtrix.org
dwibiascorrect¶
Synopsis¶
dwibiascorrect [ options ] input output
- input: The input image series to be corrected
- output: The output corrected image series
Description¶
Perform B1 field inhomogeneity correction for a DWI volume series
Options¶
- -mask Manually provide a mask image for bias field estimation
- -bias Output the estimated bias field
- -ants Use ANTS N4 to estimate the inhomogeneity field
- -fsl Use FSL FAST to estimate the inhomogeneity field
- -grad Pass the diffusion gradient table in MRtrix format
- -fslgrad bvecs bvals Pass the diffusion gradient table in FSL bvecs/bvals format
Standard options¶
- -continue <TempDir> <LastFile> Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file
- -force Force overwrite of output files if pre-existing
- -help Display help information for the script
- -nocleanup Do not delete temporary directory at script completion
- -nthreads number Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)
- -tempdir /path/to/tmp/ Manually specify the path in which to generate the temporary directory
- -quiet Suppress all console output during script execution
- -verbose Display additional information for every command invoked
References¶
fast: Zhang, Y.; Brady, M. & Smith, S. Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm. IEEE Transactions on Medical Imaging, 2001, 20, 45-57
FSL: Smith, S. M.; Jenkinson, M.; Woolrich, M. W.; Beckmann, C. F.; Behrens, T. E.; Johansen-Berg, H.; Bannister, P. R.; De Luca, M.; Drobnjak, I.; Flitney, D. E.; Niazy, R. K.; Saunders, J.; Vickers, J.; Zhang, Y.; De Stefano, N.; Brady, J. M. & Matthews, P. M. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 2004, 23, S208-S219
N4: 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
—
Author: Robert E. Smith (robert.smith@florey.edu.au)
Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors
This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/
MRtrix is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see www.mrtrix.org
dwipreproc¶
Synopsis¶
dwipreproc [ options ] pe_dir input output
- pe_dir: The phase encode direction; can be a signed axis number (e.g. -0, 1, +2) or a code (e.g. AP, LR, IS)
- input: The input DWI series to be corrected
- output: The output corrected image series
Description¶
Perform diffusion image pre-processing using FSL’s eddy tool; including inhomogeneity distortion correction using FSL’s topup tool if possible
Options¶
- -cuda Use the CUDA version of eddy
- -rpe_none Specify explicitly that no reversed phase-encoding image data is provided; eddy will perform eddy current and motion correction only
- -rpe_pair forward reverse Provide a pair of images to use for inhomogeneity field estimation; note that the FIRST of these two images must have the same phase-encode direction as the input DWIs
- -rpe_all input_revpe Provide a second DWI series identical to the input series, that has the opposite phase encoding; these will be combined in the output image
- -grad Provide a gradient table in MRtrix format
- -fslgrad bvecs bvals Provide a gradient table in FSL bvecs/bvals format
- -export_grad_mrtrix grad Export the final gradient table in MRtrix format
- -export_grad_fsl bvecs bvals Export the final gradient table in FSL bvecs/bvals format
Standard options¶
- -continue <TempDir> <LastFile> Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file
- -force Force overwrite of output files if pre-existing
- -help Display help information for the script
- -nocleanup Do not delete temporary directory at script completion
- -nthreads number Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)
- -tempdir /path/to/tmp/ Manually specify the path in which to generate the temporary directory
- -quiet Suppress all console output during script execution
- -verbose Display additional information for every command invoked
References¶
eddy: Andersson, J. L. & Sotiropoulos, S. N. An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging. NeuroImage, 2015, 125, 1063-1078
FSL: Smith, S. M.; Jenkinson, M.; Woolrich, M. W.; Beckmann, C. F.; Behrens, T. E.; Johansen-Berg, H.; Bannister, P. R.; De Luca, M.; Drobnjak, I.; Flitney, D. E.; Niazy, R. K.; Saunders, J.; Vickers, J.; Zhang, Y.; De Stefano, N.; Brady, J. M. & Matthews, P. M. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 2004, 23, S208-S219
Skare2010: Skare, S. & Bammer, R. Jacobian weighting of distortion corrected EPI data. Proceedings of the International Society for Magnetic Resonance in Medicine, 2010, 5063
topup: Andersson, J. L.; Skare, S. & Ashburner, J. How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging. NeuroImage, 2003, 20, 870-888
—
Author: Robert E. Smith (robert.smith@florey.edu.au)
Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors
This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/
MRtrix is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see www.mrtrix.org
labelsgmfix¶
Synopsis¶
labelsgmfix [ options ] parc t1 config output
- parc: The input FreeSurfer parcellation image
- t1: The T1 image to be provided to FIRST
- config: Either the FreeSurfer lookup table (if the input parcellation image is directly from FreeSurfer), or the connectome configuration file (if the parcellation image has been modified using the labelconfig command)
- output: The output parcellation image
Description¶
In a FreeSurfer parcellation image, replace the sub-cortical grey matter structure delineations using FSL FIRST
Options¶
- -premasked Indicate that brain masking has been applied to the T1 input image
- -sgm_amyg_hipp Consider the amygdalae and hippocampi as sub-cortical grey matter structures, and also replace their estimates with those from FIRST
Standard options¶
- -continue <TempDir> <LastFile> Continue the script from a previous execution; must provide the temporary directory path, and the name of the last successfully-generated file
- -force Force overwrite of output files if pre-existing
- -help Display help information for the script
- -nocleanup Do not delete temporary directory at script completion
- -nthreads number Use this number of threads in MRtrix multi-threaded applications (0 disables multi-threading)
- -tempdir /path/to/tmp/ Manually specify the path in which to generate the temporary directory
- -quiet Suppress all console output during script execution
- -verbose Display additional information for every command invoked
References¶
first: Patenaude, B.; Smith, S. M.; Kennedy, D. N. & Jenkinson, M. A Bayesian model of shape and appearance for subcortical brain segmentation. NeuroImage, 2011, 56, 907-922
FSL: Smith, S. M.; Jenkinson, M.; Woolrich, M. W.; Beckmann, C. F.; Behrens, T. E.; Johansen-Berg, H.; Bannister, P. R.; De Luca, M.; Drobnjak, I.; Flitney, D. E.; Niazy, R. K.; Saunders, J.; Vickers, J.; Zhang, Y.; De Stefano, N.; Brady, J. M. & Matthews, P. M. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 2004, 23, S208-S219
SIFT_followup: Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. The effects of SIFT on the reproducibility and biological accuracy of the structural connectome. NeuroImage, 2015, 104, 253-265
—
Author: Robert E. Smith (robert.smith@florey.edu.au)
Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors
This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/
MRtrix is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see www.mrtrix.org