This script uses the convention that, when paired, the order is always left,
right. For all methods, use enclosing for label values.
At the most basic, all you need is two surfaces (left/right .surf.gii) and a
NIFTI (.nii.gz):
python nifti_to_dscalar.py left.surf.gii right.surf.gii nifti.nii.gz
The NIFTI option is repeatable (to use the same surfaces for each one).
To use the -ribbon-enclosed mapping, simply supply the inner (WM) and outer
(pial) surface files. Two each: left, right. The default ribbon mapping is
weighted averaging, use --rc_method to change that.
usage: nifti_to_dscalar [-h] [--output_name OUTPUT_NAME [OUTPUT_NAME ...]]
[--method {trilinear,cubic,enclosing}]
[--rc_method {weighted_avg,trilinear,cubic,enclosing}]
[--inner_surfaces SURF SURF]
[--outer_surfaces SURF SURF] [--verbose]
l_surface r_surface nifti [nifti ...]
Easily project .nii.gz files into surface space.
Hemisphere order is always L->R.
positional arguments:
l_surface Left surface to map onto.
r_surface Right surface to map onto.
nifti Input NIFTI file(s)
optional arguments:
-h, --help show this help message and exit
--output_name OUTPUT_NAME [OUTPUT_NAME ...], -o OUTPUT_NAME [OUTPUT_NAME ...]
Output name (without .dscalar.nii).
Must be same length as nifti input, if provided.
--method {trilinear,cubic,enclosing}, -m {trilinear,cubic,enclosing}
Method to use.
Use 'enclosing' for labels.
Conflicts with ribbon-constrained, use --rc_method
.Default: 'trilinear'.
--rc_method {weighted_avg,trilinear,cubic,enclosing}
Method to use for ribbon-constrained mapping.
Default: 'weighted_avg'.
--inner_surfaces SURF SURF, -wm SURF SURF
WM surfaces to use ribbon enclosed projection. L/R.
Must be used with --outer_surfaces.
--outer_surfaces SURF SURF, -pial SURF SURF
Pial surfaces to use ribbon enclosed projection. L/R.
Must be used with --inner_surfaces
--verbose, -v Does what a --verbose flag usually does.