Creates pngs of standard surface and subcortical views from a nifti or cifti
input map.
Usage:
cifti_vis_map cifti-snaps [options] <map.dscalar.nii> <subject> <map-name>
cifti_vis_map nifti-snaps [options] <map.nii> <subject> <map-name>
cifti_vis_map index [options]
Arguments:
<map.dscalar.nii> A 2D cifti dscalar file to view
<map.nii> A 3D nifti file to view to view
<subject> Subject ID for HCP surfaces
<map-name> Name of dscalar map as it will appear in qc page
filenames
Options:
--qcdir PATH Full path to location of QC directory.
--hcp-data-dir PATH The directory for HCP subjects (overrides HCP_DATA
enviroment variable)
--subjects-filter STR A string that can be used to filter out subject
directories
--colour-palette STR Specify the colour palette for the seed correlation
maps
--resample-nifti The nifti file needs to be resampled to the voxel
space of the hcp subject first
--v,--verbose Verbose logging
--debug Debug logging
--help Print help
DETAILS
This makes pretty pictures of your hcp views using connectome workbenches
"show scene" commands. It pastes the pretty pictures together into some .html
QC pages. Requires connectome workbench (i.e. wb_command and imagemagick)
Also this function works by writing a temporary file into the HCP_DATA
directory, therefore, write permission in the HCP_DATA directory is required.
By default, all folder in the qc directory will be included in the index.
You can change the color palette for all pics using the --colour-palette flag.
The default colour palette is videen_style. Some people like 'PSYCH-NO-NONE'
better. For more info on palettes see wb_command help.
Written by Erin W Dickie