$ python cpac_correlations_wf.py --help
usage: cpac_correlations_wf.py [-h] [--old_outputs_path OLD_OUTPUTS_PATH]
[--new_outputs_path NEW_OUTPUTS_PATH]
[--s3_creds S3_CREDS]
[--replacements REPLACEMENTS]
[--corr_map CORR_MAP]
[--working_dir WORKING_DIR]
num_cores run_name
positional arguments:
num_cores number of cores to use - will calculate correlations
in parallel if greater than 1
run_name name for the correlations run
optional arguments:
-h, --help show this help message and exit
--old_outputs_path OLD_OUTPUTS_PATH
path to a CPAC outputs directory - the folder
containing the participant-ID labeled directories
--new_outputs_path NEW_OUTPUTS_PATH
path to a CPAC outputs directory - the folder
containing the participant-ID labeled directories
--s3_creds S3_CREDS path to your AWS S3 credentials file
--replacements REPLACEMENTS
text file containing strings you wish to have removed
from the filepaths if they occur - place one on each
line
--corr_map CORR_MAP YAML file with already-calculated correlations, which
can be provided if you only want to generate the box
plots again
--working_dir WORKING_DIR
if you are correlating two working directories of a
single participant to check intermediates$ python correlation_matrix.py --help
usage: correlation_matrix.py [-h] [--old_outputs_path OLD_OUTPUTS_PATH]
[--old_outputs_software {C-PAC,fmriprep}]
[--new_outputs_path NEW_OUTPUTS_PATH]
[--new_outputs_software {C-PAC,fmriprep}]
[--save] [--no-save]
[--subject_list SUBJECT_LIST] [--session SESSION]
[--feature_list FEATURE_LIST]
num_cores run_name
Create a correlation matrix between two C-PAC output directories.
positional arguments:
num_cores number of cores to use - will calculate correlations
in parallel if greater than 1
run_name name for the correlations run
optional arguments:
-h, --help show this help message and exit
--old_outputs_path OLD_OUTPUTS_PATH
path to an outputs directory - the folder containing
the participant-ID labeled directories
--old_outputs_software {C-PAC,fmriprep}
(default: fmriprep)
--new_outputs_path NEW_OUTPUTS_PATH
path to an outputs directory - the folder containing
the participant-ID labeled directories
--new_outputs_software {C-PAC,fmriprep}
(default: C-PAC)
--save save matrices & heatmap (default)
--no-save do not save matrices & heatmap
--subject_list SUBJECT_LIST
(default: subjects in OLD_OUTPUTS_PATH sorted by
session, subject ID). TODO: handle path to file
--session SESSION limit to a single given session (integer)
--feature_list FEATURE_LIST
TODO: handle path to file (default: ['GS', 'CSF',
'WM', 'tCompCor0', 'aCompCor0', 'aCompCor1',
'aCompCor2', 'aCompCor3', 'aCompCor4', 'FD'])
The following features currently have available definitions to calculate Pearson's r between C-PAC and fmriprep:
key feature name documentation link
-------- ------------------------ ----------------------------------------------------------------------------------
aCompCor aCompCor https://fcp-indi.github.io/docs/user/nuisance.html#acompcor
CSF mean cerebrospinal fluid https://fcp-indi.github.io/docs/user/nuisance.html#mean-white-matter-csf
FD framewise displacement https://fcp-indi.github.io/docs/user/nuisance.html#regression-of-motion-parameters
GS global signal regression https://fcp-indi.github.io/docs/user/nuisance.html#global-signal-regression
tCompCor tCompCor https://fcp-indi.github.io/docs/user/nuisance.html#tcompcor
WM mean white matter https://fcp-indi.github.io/docs/user/nuisance.html#mean-white-matter-csf