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Nipype syntax change #67

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Mar 12, 2019
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Nipype syntax change #67

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c207c9e
Create pip-delete-this-directory.txt
nrajamani3 Mar 12, 2019
e36d9c0
Create README
nrajamani3 Mar 12, 2019
60b8dc1
eddy-qc files for distortion correction
nrajamani3 Mar 12, 2019
15c61cd
added by pip
nrajamani3 Mar 12, 2019
25b07eb
Create condaRecipes
nrajamani3 Mar 12, 2019
0b0adff
delete condaRecipes
nrajamani3 Mar 12, 2019
8d02fa3
Create meta.yml
nrajamani3 Mar 12, 2019
6c55f3d
added missing files in condaRecipes
nrajamani3 Mar 12, 2019
b8e75a6
Delete meta.yaml
nrajamani3 Mar 12, 2019
8613bd0
Delete meta.yml
nrajamani3 Mar 12, 2019
34a03fe
Delete post-link.sh
nrajamani3 Mar 12, 2019
293228d
Delete pre-unlink.sh
nrajamani3 Mar 12, 2019
198c81e
Delete pip-delete-this-directory.txt
nrajamani3 Mar 12, 2019
80fd8c7
Delete README
nrajamani3 Mar 12, 2019
c7d3f6a
Delete requirements.txt
nrajamani3 Mar 12, 2019
c53f222
Delete setup.py
nrajamani3 Mar 12, 2019
231d80c
change from qc_json to out_qc_json
nrajamani3 Mar 12, 2019
44efdbc
possible change in pybids
nrajamani3 Mar 12, 2019
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16 changes: 8 additions & 8 deletions dmriprep/run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -755,13 +755,13 @@ def binarize_aparc(aparc_aseg):
wf.connect(scale_tensor_eddy, "out_file", datasink, "dmriprep.dti_eddy.@scaled_tensor")

# all the eddy_quad stuff
wf.connect(eddy_quad, 'qc_json', datasink, "dmriprep.qc.@eddyquad_json")
wf.connect(eddy_quad, 'qc_pdf', datasink, "dmriprep.qc.@eddyquad_pdf")
wf.connect(eddy_quad, 'avg_b_png', datasink, "dmriprep.qc.@eddyquad_bpng")
wf.connect(eddy_quad, 'avg_b0_pe_png', datasink, "dmriprep.qc.@eddyquad_b0png")
wf.connect(eddy_quad, 'cnr_png', datasink, "dmriprep.qc.@eddyquad_cnr")
wf.connect(eddy_quad, 'vdm_png', datasink, "dmriprep.qc.@eddyquad_vdm")
wf.connect(eddy_quad, 'residuals', datasink, 'dmriprep.qc.@eddyquad_resid')
wf.connect(eddy_quad, 'out_qc_json', datasink, "dmriprep.qc.@eddyquad_json")
wf.connect(eddy_quad, 'out_qc_pdf', datasink, "dmriprep.qc.@eddyquad_pdf")
wf.connect(eddy_quad, 'out_avg_b_png', datasink, "dmriprep.qc.@eddyquad_bpng")
wf.connect(eddy_quad, 'out_avg_b0_pe_png', datasink, "dmriprep.qc.@eddyquad_b0png")
wf.connect(eddy_quad, 'out_cnr_png', datasink, "dmriprep.qc.@eddyquad_cnr")
wf.connect(eddy_quad, 'out_vdm_png', datasink, "dmriprep.qc.@eddyquad_vdm")
wf.connect(eddy_quad, 'out_residuals', datasink, 'dmriprep.qc.@eddyquad_resid')

# anatomical registration stuff
wf.connect(bbreg, "min_cost_file", datasink, "dmriprep.reg.@mincost")
Expand Down Expand Up @@ -793,7 +793,7 @@ def report_fn(dwi_corrected_file, eddy_rms, eddy_report,

# for the report, lets show the eddy corrected (full volume) image
wf.connect(voltransform, "transformed_file", report_node, 'dwi_corrected_file')
wf.connect(eddy_quad, 'qc_json', report_node, 'eddy_qc_file')
wf.connect(eddy_quad, 'out_qc_json', report_node, 'eddy_qc_file')

# add the rms movement output from eddy
wf.connect(prep, "fsl_eddy.out_movement_rms", report_node, 'eddy_rms')
Expand Down