ciftify_vol_result

Projects a result (or atlas) in nifti space to a surface and subcortical masks.

Usage:
  ciftify_vol_result [options] <subject> <vol.nii.gz> <output.dscalar.nii>

Arguments:
    <subject>              The subject ID for the surfaces to project to.
    <vol.nii.gz>           Nifty volume to project to cifti space
    <output.dscalar.nii>   Output dscalar.nii image

Options:
  --hcp-data-dir PATH      Path to the hcp data directory. (Overides HCP_DATA environment variable)
  --integer-labels         The nifti input file contains integer label values
  --surface-vol NII        Specify a separate volume for surface projection than <vol.nii.gz>
  --subcortical-vol NII    Specify a separate volume for subcortical masks than <vol.nii.gz>
  --dilate mm              Run cifti-dilate with a specified mm
  --HCP-Pipelines          Indicates that the surfaces were generated by the HCP-Pipelines
  --HCP-MSMAll             Project to the MSMAll surface (instead of '32k_fs_LR', only works for HCP subjects)
  --resample-nifti         Use this argument to resample voxels 2x2x2 before projecting
  --debug                  Debug logging in Erin's very verbose style
  -n,--dry-run             Dry run
  -h,--help                Print help

DETAILS
This projects the nifti data to the surfaces from the MNINonLinear/32k_fs_LR space in hcp
for a given subject (the space used for fMRI analysis). This assumes that the HCP_DATA
folder was created with ciftify_recon_all. If the HCP_DATA was created using the
HCP pipelines (for example the HCP-dataset), use "--HCP-subject" option.

The "--surface-vol" and "--subcortical-vol" options were added so that you can specify
separate input nifty volumes for masks one the surface and for subcortical space.
(For example, so that a large hippocampus cluster is not projected to the nearby cortical surface).
If they are not given, <vol.nii.gz> will be used as the input volume for their steps.

The "--dilate" option will add a can to wb_commands -cifti-dilate function
(with the specified mm option) to expand clusters and fill holes.

If <subject> is set to 'HCP_S1200_GroupAvg' the volume with project to the surfaces
of the HCP S900 release Average subject.  This 'average fiducial mapping' approach
is not recommended in most cases, as group average surfaces do not encapsulate
all of the gray matter cortical ribbon.

(see https://github.com/edickie/ciftify/wiki/ciftify_vol_result-usage)

Written by Erin W Dickie, Mar 1, 2016