Major refactoring to match future MRtrix 3.1.0

mrtrix3_connectome/__init__.py

@@ -0,0 +1,10 @@
+import os
+IS_CONTAINER = os.path.exists('/version') \
+               and os.path.exists('/mrtrix3_version')
+OPTION_PREFIX = '--' if IS_CONTAINER else '-'
+
+# pylint: disable=consider-using-with
+__version__ = 'BIDS-App \'MRtrix3_connectome\'' \
+              f'version {open("/version", "r", encoding="utf-8").read()}' \
+              if IS_CONTAINER \
+              else 'BIDS-App \'MRtrix3_connectome\' standalone'

mrtrix3_connectome/anat/shared.py

@@ -0,0 +1,24 @@
+import shutil
+from mrtrix3 import MRtrixError
+from mrtrix3 import app
+from mrtrix3 import fsl
+
+class Shared(object): #pylint: disable=useless-object-inheritance
+    def __init__(self, gdc_images):
+        self.gdc_images = gdc_images
+        try:
+            self.fsl_anat_cmd = shutil.which(fsl.exe_name('fsl_anat'))
+        except MRtrixError:
+            self.fsl_anat_cmd = None
+        robex_cmd = shutil.which('ROBEX')
+        self.robex_cmd = robex_cmd if robex_cmd else shutil.which('runROBEX.sh')
+        self.n4_cmd = shutil.which('N4BiasFieldCorrection')
+        self.synthstrip_cmd = shutil.which('mri_synthstrip')
+
+        if not self.fsl_anat_cmd and not self.robex_cmd and not self.synthstrip_cmd:
+            app.warn('No commands for T1w image processing found; '
+                     'command can only proceed if either '
+                     'existing pre-processed T1w image data can be found, '
+                     'or if doing preproc-level analysis '
+                     'where registration of DWI to T1-weighted image data '
+                     'will be excluded from processing')

mrtrix3_connectome/citations.py

@@ -0,0 +1,294 @@
+def add_citations(cmdline, option_prefix='-'):
+    cmdline.add_citation(
+        'Smith, R. E.; Connelly, A. '
+        'MRtrix3_connectome: A BIDS Application for quantitative structural '
+        'connectome construction. '
+        'In Proc OHBM, 2019, W610',
+        is_external=False)
+    cmdline.add_citation(
+        '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',
+        condition='If performing preproc-level analysis',
+        is_external=True)
+    cmdline.add_citation(
+        'Andersson, J. L. R.; Jenkinson, M. & Smith, S. '
+        'Non-linear registration, aka spatial normalisation. '
+        'FMRIB technical report, 2010, TR07JA2',
+        condition='If performing participant-level analysis '
+                  + f'using {option_prefix}template_reg fsl',
+        is_external=True)
+    cmdline.add_citation(
+        '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',
+        condition='If performing preproc-level analysis',
+        is_external=True)
+    cmdline.add_citation(
+        'Andersson, J. L. R.; Graham, M. S.; Zsoldos, E. '
+        '& Sotiropoulos, S. N. '
+        'Incorporating outlier detection and replacement into a '
+        'non-parametric framework for movement and distortion correction of '
+        'diffusion MR images. '
+        'NeuroImage, 2016, 141, 556-572',
+        condition='If performing preproc-level analysis',
+        is_external=True)
+    cmdline.add_citation(
+        'Andersson, J. L. R.; Graham, M. S.; Drobnjak, I.; Zhang, H.; '
+        'Filippini, N. & Bastiani, M. '
+        'Towards a comprehensive framework for movement and distortion '
+        'correction of diffusion MR images: Within volume movement. '
+        'NeuroImage, 2017, 152, 450-466',
+        condition='If performing preproc-level analysis '
+                  'utilising slice-to-volume motion correction',
+        is_external=True)
+    cmdline.add_citation(
+        'Andersson, J. L. R.; Graham,, M. S.; Drobnjak, I.; Zhang, H. & '
+        'Campbell, J. '
+        'Susceptibility-induced distortion that varies due to motion: '
+        'Correction in diffusion MR without acquiring additional data. '
+        'NeuroImage, 2018, 171, 277-295',
+        condition='If performing preproc-level analysis',
+        is_external=True)
+    cmdline.add_citation(
+        'Avants, B. B.; Epstein, C. L.; Grossman, M.; Gee, J. C. '
+        'Symmetric diffeomorphic image registration with cross-correlation: '
+        'Evaluating automated labeling of elderly and neurodegenerative brain. '
+        'Medical Image Analysis, 2008, 12, 26-41',
+        condition='If performing participant-level analysis, '
+        f'using {option_prefix}parcellation [ aal, aal2, '
+        'brainnetome246mni, craddock200, craddock400, perry512, '
+        'yeo7mni or yeo17mni ], '
+        f'and not using {option_prefix}template_reg fsl',
+        is_external=True)
+    cmdline.add_citation(
+        'Bhushan, C.; Haldar, J. P.; Choi, S.; Joshi, A. A.; Shattuck, D. W. & '
+        'Leahy, R. M. '
+        'Co-registration and distortion correction of diffusion and anatomical '
+        'images based on inverse contrast normalization. '
+        'NeuroImage, 2015, 115, 269-280',
+        condition='If performing preproc-level analysis',
+        is_external=True)
+    cmdline.add_citation(
+        'Craddock, R. C.; James, G. A.; Holtzheimer, P. E.; Hu, X. P.; '
+        'Mayberg, H. S. '
+        'A whole brain fMRI atlas generated via spatially constrained '
+        'spectral clustering. '
+        'Human Brain Mapping, 2012, 33(8), 1914-1928',
+        condition='If performing participant-level analysis and '
+        f'using {option_prefix}parcellation '
+        '[ craddock200 or craddock400 ]',
+        is_external=True)
+    cmdline.add_citation(
+        'Dale, A. M.; Fischl, B. & Sereno, M. I. '
+        'Cortical Surface-Based Analysis: '
+        'I. Segmentation and Surface Reconstruction. '
+        'NeuroImage, 1999, 9, 179-194',
+        condition='If performing participant-level analysis and '
+        f'using {option_prefix}parcellation '
+        '[ brainnetome246fs, desikan, destrieux, hcpmmp1, '
+        'yeo7fs or yeo17fs ]',
+        is_external=True)
+    cmdline.add_citation(
+        'Desikan, R. S.; Segonne, F.; Fischl, B.; Quinn, B. T.; '
+        'Dickerson, B. C.; Blacker, D.; Buckner, R. L.; Dale, A. M.; '
+        'Maguire, R. P.; Hyman, B. T.; Albert, M. S. & Killiany, R. J. '
+        'An automated labeling system for subdividing the human cerebral '
+        'cortex on MRI scans into gyral based regions of interest. '
+        'NeuroImage, 2006, 31, 968-980',
+        condition='If performing participant-level analysis and '
+        f'using {option_prefix}parcellation desikan',
+        is_external=True)
+    cmdline.add_citation(
+        'Destrieux, C.; Fischl, B.; Dale, A. & Halgren, E. '
+        'Automatic parcellation of human cortical gyri and sulci using '
+        'standard anatomical nomenclature. '
+        'NeuroImage, 2010, 53, 1-15',
+        condition='If performing participant-level analysis and '
+        f'using {option_prefix}parcellation destrieux',
+        is_external=True)
+    cmdline.add_citation(
+        'Fan, L.; Li, H.; Zhuo, J.; Zhang, Y.; Wang, J.; Chen, L.; Yang, Z.; '
+        'Chu, C.; Xie, S.; Laird, A.R.; Fox, P.T.; Eickhoff, S.B.; Yu, C.; '
+        'Jiang, T. '
+        'The Human Brainnetome Atlas: '
+        'A New Brain Atlas Based on Connectional Architecture. '
+        'Cerebral Cortex, 2016, 26 (8), 3508-3526',
+        condition='If performing participant-level analysis and '
+        f'using {option_prefix}parcellation '
+        '[ brainnetome246fs brainnetome246mni ]',
+        is_external=True)
+    cmdline.add_citation(
+        'Glasser, M. F.; Coalson, T. S.; Robinson, E. C.; Hacker, C. D.; '
+        'Harwell, J.; Yacoub, E.; Ugurbil, K.; Andersson, J.; Beckmann, C. F.; '
+        'Jenkinson, M.; Smith, S. M. & Van Essen, D. C. '
+        'A multi-modal parcellation of human cerebral cortex. '
+        'Nature, 2016, 536, 171-178',
+        condition='If performing participant-level analysis and '
+        f'using {option_prefix}parcellation hcpmmp1',
+        is_external=True)
+    cmdline.add_citation(
+        'Iglesias, J. E.; Liu, C. Y.; Thompson, P. M. & Tu, Z. '
+        'Robust Brain Extraction Across Datasets and '
+        'Comparison With Publicly Available Methods. '
+        'IEEE Transactions on Medical Imaging, 2011, 30, 1617-1634',
+        condition='If performing either preproc-level or participant-level '
+        'analysis and ROBEX is used for T1w brain extraction',
+        is_external=True)
+    cmdline.add_citation(
+        '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',
+        condition='If performing either preproc-level '
+        'or participant-level analysis',
+        is_external=False)
+    cmdline.add_citation(
+        'Kellner, E.; Dhital, B.; Kiselev, V. G.; Reisert, M. '
+        'Gibbs-ringing artifact removal based on local subvoxel-shifts. '
+        'Magnetic Resonance in Medicine, 2006, 76(5), 1574-1581',
+        condition='If performing preproc-level analysis',
+        is_external=True)
+    cmdline.add_citation(
+        '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',
+        condition='If performing participant-level analysis and '
+        f'not using {option_prefix}parcellation '
+        '[ brainnetome246fs or brainnetome246mni ]',
+        is_external=True)
+    cmdline.add_citation(
+        'Perry, A.; Wen, W.; Kochan, N. A.; Thalamuthu, A.; Sachdev, P. S.; '
+        'Breakspear, M. '
+        'The independent influences of age and education on functional brain '
+        'networks and cognition in healthy older adults. '
+        'Human Brain Mapping, 2017, 38(10), 5094-5114',
+        condition='If performing participant-level analysis and '
+        f'using {option_prefix}parcellation perry512',
+        is_external=True)
+    cmdline.add_citation(
+        'Smith, S. M. '
+        'Fast robust automated brain extraction. '
+        'Human Brain Mapping, 2002, 17, 143-155',
+        condition='If performing either preproc-level or participant-level '
+        'analysis and FSL is used for T1w brain extraction',
+        is_external=True)
+    cmdline.add_citation(
+        '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',
+        condition='If performing participant-level analysis',
+        is_external=False)
+    cmdline.add_citation(
+        '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, 2015a, 104, 253-265',
+        condition='If performing participant-level analysis',
+        is_external=False)
+    cmdline.add_citation(
+        'Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. '
+        'SIFT2: Enabling dense quantitative assessment of brain white matter '
+        'connectivity using streamlines tractography. '
+        'NeuroImage, 2015b, 119, 338-351',
+        condition='If performing participant-level analysis',
+        is_external=False)
+    cmdline.add_citation(
+        'Smith, R. E.; Raffelt, D.; Tournier, J.-D.; Connelly, A. '
+        'Quantitative streamlines tractography: Methods and inter-subject '
+        'normalisation. '
+        'OHBM Aperture, 2022, doi: 10.52294/ApertureNeuro.2022.2.NEOD9565',
+        condition='If performing group-level analysis',
+        is_external=False)
+    cmdline.add_citation(
+        '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',
+        condition='If performing either preproc-level or participant-level '
+        'analysis',
+        is_external=False)
+    cmdline.add_citation(
+        'Tournier, J.-D.; Calamante, F. & Connelly, A. '
+        'Improved probabilistic streamlines tractography by 2nd order '
+        'integration over fibre orientation distributions. '
+        'Proceedings of the International Society for Magnetic '
+        'Resonance in Medicine, 2010, 1670',
+        condition='If performing participant-level analysis '
+        f'and {option_prefix}streamlines 0 is not set',
+        is_external=False)
+    cmdline.add_citation(
+        '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',
+        condition='If performing either preproc-level or participant-level '
+        'analysis, and N4 is used for either DWI or T1w bias field correction',
+        is_external=True)
+    cmdline.add_citation(
+        'Tustison, N.; Avants, B. '
+        'Explicit B-spline regularization in diffeomorphic image '
+        'registration. '
+        'Frontiers in Neuroinformatics, 2013, 7, 39',
+        condition='If performing participant-level analysis, '
+        f'using {option_prefix}parcellation [ aal, aal2, '
+        'brainnetome246mni, craddock200, craddock400, perry512, '
+        'yeo7mni or yeo17mni ], '
+        f'and not using {option_prefix}template_reg fsl',
+        is_external=True)
+    cmdline.add_citation(
+        'Tzourio-Mazoyer, N.; Landeau, B.; Papathanassiou, D.; Crivello, F.; '
+        'Etard, O.; Delcroix, N.; Mazoyer, B. & Joliot, M. '
+        'Automated Anatomical Labeling of activations in SPM using a '
+        'Macroscopic Anatomical Parcellation of the MNI MRI '
+        'single-subject brain. '
+        'NeuroImage, 15(1), 273-289',
+        condition='If performing participant-level analysis '
+        f'and using {option_prefix}parcellation [ aal or aal2 ]',
+        is_external=True)
+    cmdline.add_citation(
+        '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',
+        condition='If performing preproc-level analysis',
+        is_external=False)
+    cmdline.add_citation(
+        'Yeh, C.H.; Smith, R.E.; Liang, X.; Calamante, F.; Connelly, A. '
+        'Correction for diffusion MRI fibre tracking biases: '
+        'The consequences for structural connectomic metrics. '
+        'Neuroimage, 2016, 142, 150-162',
+        condition='If utilising connectome outputs from '
+        'participant-level analysis',
+        is_external=False)
+    cmdline.add_citation(
+        'Yeo, B.T.; Krienen, F.M.; Sepulcre, J.; Sabuncu, M.R.; Lashkari, D.; '
+        'Hollinshead, M.; Roffman, J.L.; Smoller, J.W.; Zollei, L.; '
+        'Polimeni, J.R.; Fischl, B.; Liu, H. & Buckner, R.L. '
+        'The organization of the human cerebral cortex estimated by '
+        'intrinsic functional connectivity. '
+        'J Neurophysiol, 2011, 106(3), 1125-1165',
+        condition='If performing participant-level analysis '
+        f'and using {option_prefix}parcellation '
+        '[ yeo7fs, yeo7mni, yeo17fs or yeo17mni ]',
+        is_external=False)
+    cmdline.add_citation(
+        'Zalesky, A.; Fornito, A.; Harding, I. H.; Cocchi, L.; Yucel, M.; '
+        'Pantelis, C. & Bullmore, E. T. '
+        'Whole-brain anatomical networks: Does the choice of nodes matter? '
+        'NeuroImage, 2010, 50, 970-983',
+        condition='If performing participant-level analysis '
+        'and using {option_prefix}parcellation perry512',
+        is_external=True)
+    cmdline.add_citation(
+        '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',
+        condition='If performing participant-level analysis',
+        is_external=True)