Commit e6fdd775 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

MNT: separate "fmrib" from "fmrib_cats", add new "fmrib_standard" for normal

processing run
parent 9d35a714
......@@ -6,7 +6,7 @@
# Use local settings
config_file local
config_file local
#
......@@ -37,26 +37,19 @@ config_file local
# Suppress with `-sp`
# - NA insertion
datacoding_file fmrib/datacodings_navalues.tsv
datacoding_file fmrib/datacodings_navalues.tsv
# - Categorical recoding
datacoding_file fmrib/datacodings_recoding.tsv
datacoding_file fmrib/datacodings_recoding.tsv
# - Cleaning
variable_file fmrib/variables_clean.tsv
variable_file fmrib/variables_clean.tsv
# - Child value replacement
variable_file fmrib/variables_parentvalues.tsv
variable_file fmrib/variables_parentvalues.tsv
# - Processing
processing_file fmrib/processing.tsv
processing_file fmrib/processing.tsv
#
# FMRIB Categories
#
# FMRIB-curated categories, largely drawn from showcase categories, with default
# suggested subset to use
#
category_file fmrib/categories.tsv
# Select useful categories
config_file fmrib_cats
# FMRIB-curated categories, largely drawn from showcase categories
category_file fmrib/categories.tsv
#
......@@ -68,10 +61,10 @@ config_file fmrib_cats
# within these hours.
#
plugin_file fmrib
date_format FMRIBImagingDate
time_format FMRIBImagingTime
plugin_file fmrib
date_format FMRIBImagingDate
time_format FMRIBImagingTime
# Only save numeric columns to the main output file
# Drop non-numeric columns - the main output file only contains numeric data.
suppress_non_numerics
#
# FUNPACK "fmrib_cats.cfg" configuration file
#
# Provides recommended set of categories to process, from full list of
# Provides recommended set of categories to process, from full list of
# FMRIB-curated categories (see funpack/configs/fmrib/categories.tsv)
#
category 1
category 2
category 3
category 10
category 11
category 12
category 13
category 14
category 20
category 21
category 22
category 23
category 24
category 25
category 26
category 30
category 32
category 50
category 51
category 60
category 70
category 98
category 99
category 1
category 2
category 3
category 10
category 11
category 12
category 13
category 14
category 20
category 21
category 22
category 23
category 24
category 25
category 26
category 30
category 32
category 50
category 51
category 60
category 70
category 98
category 99
......@@ -7,8 +7,10 @@
# separate file containing summary information about these variables.
#
# base this config on fmrib_logs
# base this config on fmrib_logs,
# and include all fmrib categories
config_file fmrib_logs
config_file fmrib_cats
# Include unknown/uncategorised variables
category unknown
......
#
# FUNPACK "fmrib_standard.cfg" configuration file
#
# This is the configuration used for standard internal FMRIB runs.
config_file fmrib_logs
config_file fmrib_cats
......@@ -7,8 +7,8 @@
# Overwrite files
overwrite
# Number of cores to use in parallelisation; -1 for 'all possible'
num_jobs -1
# Number of cores to use in parallelisation; -1 for 'all possible'
num_jobs -1
# It is always recommended to trust data types of each column; without this option
# processing is considerably slower. Disable when debugging a possibly prolematic file.
......
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