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josephmjejosephmje
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update docs
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‎CHANGES.rst

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Original file line numberDiff line numberDiff line change
@@ -4,6 +4,7 @@ Upcoming release (TBD)
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0.2.0 (September 6, 2019)
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=======================
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* ENH: Add workflows for ANTs and BrainSuite nonlinear registration-based distortion correction
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* ENH: Add workflow for concatenating dwi scans based on ``--concat_dwis`` list
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* ENH: Enable parallel processing of nodes
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* ENH: Run ``bids-validator`` before pipeline start

‎dmriprep/workflows/dwi/base.py

Lines changed: 34 additions & 69 deletions
Original file line numberDiff line numberDiff line change
@@ -44,21 +44,7 @@ def init_dwi_preproc_wf(
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from collections import namedtuple
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from dmriprep.workflows.dwi import init_dwi_preproc_wf
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BIDSLayout = namedtuple('BIDSLayout', ['root'])
47-
wf = init_dwi_preproc_wf(
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layout=BIDSLayout('.'),
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output_dir='.',
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subject_id='dmripreptest',
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dwi_file='/madeup/path/sub-01_dwi.nii.gz',
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metadata={},
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b0_thresh=5,
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output_resolution=(1, 1, 1),
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bet_dwi=0.3,
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bet_mag=0.3,
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acqp_file='',
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omp_nthreads=1,
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ignore=[],
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synb0_dir=''
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)
47+
wf = init_dwi_preproc_wf(layout=BIDSLayout('.'), output_dir='.', subject_id='dmripreptest', dwi_file='/madeup/path/sub-01_dwi.nii.gz', metadata={'PhaseEncodingDirection': 'j-', 'TotalReadoutTime': 0.05}, b0_thresh=5, output_resolution=(1, 1, 1), bet_dwi=0.3, bet_mag=0.3, acqp_file='', omp_nthreads=1, ignore=['fieldmaps'], synb0_dir='')
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"""
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@@ -314,7 +300,6 @@ def get_b0_mask_fn(b0_file):
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('bvec_file', 'in_bvec')]),
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(bet_dwi0, ecc, [('mask_file', 'in_mask')]),
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(gen_idx, ecc, [('out_file', 'in_index')]),
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(acqp, ecc, [('out_file', 'in_acqp')]),
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(ecc, denoise_eddy, [('out_corrected', 'in_file')]),
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(ecc, bias_correct, [('out_corrected', 'in_file'),
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('out_rotated_bvecs', 'in_bvec')]),
@@ -327,13 +312,21 @@ def get_b0_mask_fn(b0_file):
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(inputnode, eddy_quad, [('bval_file', 'bval_file')]),
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(b0mask_node, eddy_quad, [('mask_file', 'mask_file')]),
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(gen_idx, eddy_quad, [('out_file', 'idx_file')]),
330-
(acqp, eddy_quad, [('out_file', 'param_file')]),
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(inputnode, tensor_wf, [('bval_file', 'inputnode.bval_file')]),
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(b0mask_node, tensor_wf, [('mask_file', 'inputnode.mask_file')]),
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(ecc, tensor_wf, [('out_corrected', 'inputnode.dwi_file'),
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('out_rotated_bvecs', 'inputnode.bvec_file')])
335319
])
336320

321+
if acqp_file:
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ecc.inputs.in_acqp = acqp_file
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eddy_quad.inputs.param_file = acqp_file
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else:
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dwi_wf.connect([
326+
(acqp, ecc, [('out_file', 'in_acqp')]),
327+
(acqp, eddy_quad, [('out_file', 'param_file')])
328+
])
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337330
# # If synb0 is meant to be used
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# if synb0_dir:
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# dwi_wf.connect(
@@ -360,63 +353,35 @@ def get_b0_mask_fn(b0_file):
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fmap = fmaps[0]
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# Else If epi files detected
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if fmap['suffix'] == 'epi':
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dwi_wf.connect(
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[
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(
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sdc_wf,
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ecc,
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[
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('outputnode.out_topup', 'in_topup_fieldcoef'),
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#('outputnode.out_enc_file', 'in_acqp'),
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('outputnode.out_movpar', 'in_topup_movpar'),
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],
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),
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# (
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# sdc_wf,
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# eddy_quad,
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# [('outputnode.out_enc_file', 'param_file')],
378-
# ),
379-
]
380-
)
356+
dwi_wf.connect([
357+
(sdc_wf, ecc, [('outputnode.out_topup', 'in_topup_fieldcoef'),
358+
('outputnode.out_movpar', 'in_topup_movpar')])
359+
])
381360
# Otherwise (fieldmaps)
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else:
383362
dwi_wf.connect([
384363
(bet_dwi0, sdc_wf, [('out_file', 'inputnode.b0_stripped')]),
385-
(sdc_wf, ecc, [('outputnode.out_fmap', 'field')]),
386-
#(acqp, ecc, [('out_file', 'in_acqp')]),
387-
# (acqp, eddy_quad, [('out_file', 'param_file')]),
388-
]
389-
)
364+
(sdc_wf, ecc, [('outputnode.out_fmap', 'field')])
365+
])
390366

391-
dwi_wf.connect(
392-
[
393-
(ecc, outputnode, [('out_corrected', 'out_dwi')]),
394-
(inputnode, outputnode, [('bval_file', 'out_bval')]),
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(ecc, outputnode, [('out_rotated_bvecs', 'out_bvec')]),
396-
(gen_idx, outputnode, [('out_file', 'index')]),
397-
(acqp, outputnode, [('out_file', 'acq_params')]),
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(b0mask_node, outputnode, [('mask_file', 'out_mask')]),
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(avg_b0_0, outputnode, [('out_file', 'out_b0_pre')]),
400-
(bet_dwi0, outputnode, [('mask_file', 'out_b0_mask_pre')]),
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(
402-
eddy_quad,
403-
outputnode,
404-
[('qc_json', 'out_eddy_quad_json'), ('qc_pdf', 'out_eddy_quad_pdf')],
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),
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(
407-
tensor_wf,
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outputnode,
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[
410-
('outputnode.FA_file', 'out_dtifit_FA'),
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('outputnode.MD_file', 'out_dtifit_MD'),
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('outputnode.AD_file', 'out_dtifit_AD'),
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('outputnode.RD_file', 'out_dtifit_RD'),
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('outputnode.V1_file', 'out_dtifit_V1'),
415-
('outputnode.sse_file', 'out_dtifit_sse'),
416-
],
417-
),
418-
]
419-
)
367+
dwi_wf.connect([
368+
(ecc, outputnode, [('out_corrected', 'out_dwi')]),
369+
(inputnode, outputnode, [('bval_file', 'out_bval')]),
370+
(ecc, outputnode, [('out_rotated_bvecs', 'out_bvec')]),
371+
(gen_idx, outputnode, [('out_file', 'index')]),
372+
(acqp, outputnode, [('out_file', 'acq_params')]),
373+
(b0mask_node, outputnode, [('mask_file', 'out_mask')]),
374+
(avg_b0_0, outputnode, [('out_file', 'out_b0_pre')]),
375+
(bet_dwi0, outputnode, [('mask_file', 'out_b0_mask_pre')]),
376+
(eddy_quad, outputnode, [('qc_json', 'out_eddy_quad_json'),
377+
('qc_pdf', 'out_eddy_quad_pdf')]),
378+
(tensor_wf, outputnode, [('outputnode.FA_file', 'out_dtifit_FA'),
379+
('outputnode.MD_file', 'out_dtifit_MD'),
380+
('outputnode.AD_file', 'out_dtifit_AD'),
381+
('outputnode.RD_file', 'out_dtifit_RD'),
382+
('outputnode.V1_file', 'out_dtifit_V1'),
383+
('outputnode.sse_file', 'out_dtifit_sse')])
384+
])
420385

421386
return dwi_wf
422387

‎docs/dmriprep.workflows.fieldmap.rst

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@@ -4,6 +4,14 @@ dmriprep.workflows.fieldmap package
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Submodules
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----------
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7+
dmriprep.workflows.fieldmap.ants module
8+
---------------------------------------
9+
10+
.. automodule:: dmriprep.workflows.fieldmap.ants
11+
:members:
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:undoc-members:
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:show-inheritance:
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715
dmriprep.workflows.fieldmap.base module
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---------------------------------------
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‎docs/outputs.rst

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@@ -16,3 +16,31 @@ Preprocessed data (dMRIPrep *derivatives*)
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Anatomical derivatives are placed in each subject's ``anat`` subfolder:
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Diffusion derivatives are stored in the ``dwi`` subfolder.
19+
20+
.. code-block:: console
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22+
dmriprep/
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sub-001/
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ses-01/
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dwi/
26+
# preprocessed diffusion weighted images
27+
sub-001_ses-01_desc-preproc.dwi.nii.gz
28+
sub-001_ses-01_desc-preproc.dwi.bval
29+
sub-001_ses-01_desc-preproc.dwi.bvec
30+
sub-001_ses-01_desc-preproc.dwi.json
31+
# mask
32+
sub-001_ses-01_desc-brain_mask.nii.gz
33+
# model-derived maps
34+
sub-001_ses-01_model-DTI_desc-preproc_FA.nii.gz
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sub-001_ses-01_model-DTI_desc-preproc_MD.nii.gz
36+
sub-001_ses-01_model-DTI_desc-preproc_AD.nii.gz
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sub-001_ses-01_model-DTI_desc-preproc_RD.nii.gz
38+
# directionally-encoded colour (DEC) maps
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sub-001_ses-01_model-DTI_desc-DEC_FA.nii.gz
40+
# grey/white matter masks
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sub-001_ses-01_desc-aparcaseg_dseg.nii.gz
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sub-001_ses-01_desc-aseg_dseg.nii.gz
43+
anat/
44+
dataset_description.json
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sub-001.html
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index.html

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