- generate eccentricity x polar angle parcellations
- scripts:
- parcellation-generator-main.sh
- polar-angle-by-eccentricity-nifti-generator.sh
- inputs:
- prfSurfacesDir
- prfVerticesDir
- min_degree_PA
- max_degree_PA
- min_degree_ECC
- max_degree_ECC
- freesurfer
- inputparc
- dwi
- inputs:
- combine-parcellation.sh
- inputs:
- min_degree_PA
- max_degree_PA
- min_degree_ECC
- max_degree_ECC
- inputs:
- polar-angle-by-eccentricity-nifti-generator.sh
- parcellation-generator-main.sh
- for now, hard-set ecc and polar angle bins (for meridian analysis)
- polar angle: 0-20, 35-55, 80-100, 125-145, 160-180 (5)
- eccentricity: 0-1, 1-2, 2-3, 3-4, 4-5, 5-6, 6-7, 7-8, 8-90 (9)
- total number of parcellations: 45
- for future, will want to be able to sweep across x degree sweeps
- polar angle: +/- 10 degrees, +/- 20 degrees
- eccentricity: +/- 1 degree
- scripts:
- segment streamlines that connect within each ecc x polar angle parcellation
- scripts:
- tract-segmentation-main.sh
- initial-tract-segment.sh
- inputs:
- track
- both_endpoints
- inputs:
- cleanup-assignments.py
- final-tract-segment.sh
- inputs:
- track
- inputs:
- initial-tract-segment.sh
- tract-segmentation-main.sh
- 45 total tractograms
- scripts:
- generate connectivity matrices for each ecc x polar angle parcellation
- scripts:
- scmrt-connectivity-main.sh
- extract-streamline-weights.py (skipping for now)
- inputs:
- labels
- weights
- will only run if both labels & weights exist.
- inputs:
- generate-connectomes.sh
- inputs:
- varea_parc
- varea_label
- assignment_radial_search
- assignment_reverse_search
- assignment_forward_search
- length_vs_invlength
- inputs:
- update-assignments.py
- extract-streamline-weights.py (skipping for now)
- scmrt-connectivity-main.sh
- output as conmats
- similarity measures (6 total)
- count, length, inv length, density, den len, den inv len
- scripts:
- generate network datatypes
- scripts:
- network-generator- main.sh
- network-generator.py
- network-generator- main.sh
- one for each ecc x polar angle parcellation (45)
- one for each similarity measure (6)
- scripts:
- compute network measurements on each network datatype
- scripts:
- network-measurements-main.sh
- network-measurements.py
- inputs:
- richClubPercentage
- inputs:
- clean-up-file-names.py
- network-measurements.py
- network-measurements-main.sh
- scripts:
- create cortexmap datatype
- scripts:
- cortexmap-generator-main.sh
- cortex-mapping-pipeline.sh
- cortexmap-generator-main.sh
- scripts:
- create wmc datatype for all generated connectome tracts
- scripts:
- wmc-generator-main.sh
- generate-wmc.py
- parcellation2vtk.py
- wmc-generator-main.sh
- scripts:
- generate dataframes of network statistics
- scripts: -netstats-generator-main.sh -generate-netstats.py
- parcellation-generator-main.sh
- inputs in config for this section:
- prfSurfacesDir
- prfVerticesDir
- min_degree_PA
- max_degree_PA
- min_degree_ECC
- max_degree_ECC
- freesurfer
- inputparc
- dwi
- inputs in config for this section:
- tract-segmentation-main.sh
- inputs in config for this section:
- track
- both_endpoints
- inputs in config for this section:
- scmrt-connectivity-main.sh
- inputs in config for this section:
- varea_parc
- varea_label
- assignment_radial_search
- assignment_reverse_search
- assignment_forward_search
- length_vs_invlength
- not being used:
- labels
- weights
- inputs in config for this section:
- network-generator-main.sh
- no configurable inputs. everything comes from previous scripts
- network-measurements-main.sh
- inputs in config for this section:
- richClubPercentage
- inputs in config for this section:
- cortexmap-generator-main.sh
- wmc-generator-main.sh
- netstats-generator-main.sh
{
"prfSurfacesDir": "input/prf/prf_surfaces",
"prfVerticesDir": "input/prf/prf_verts,
"freesurfer": "input/freesurfer/output",
"inputparc": "aparc.a2009s",
"dwi": "input/dwi/dwi.nii.gz",
"track": "input/track/track.tck",
"varea_parc": "input/varea/parc.nii.gz",
"varea_label": "input/varea/label.json",
"min_degree_PA": "0 35 80 125 160",
"max_degree_PA": "20 55 100 145 180",
"min_degree_ECC": "0 1 2 3 4 5 6 7 8",
"max_degree_ECC": "1 2 3 4 5 6 7 8 90",
"both_endpoints": "true",
"assignment_radial_search": 4,
"assignment_reverse_search": "",
"assignment_forward_search": "",
"length_vs_invlength": "true",
"labels": "",
"weights": "",
"richClubPercentage": 90,
"analysis": "polarAngleMeridiansConnectomics",
"_inputs": [
{
"meta": {
"subject": "CC520287"
}
}
]
}
- neuro/conmats
- generic/networks
- neuro/parcellation/volume
- neuro/cortexmap
- neuro/track/tck
- neuro/tcks
- raw
- neuro/wmc
- neuro/net-stats