Standard and nonstandard spaces
The command line interface of ASLPPrep allows resampling of the pre-processed
and computed CBF maps onto other output spaces.
That is achieved using the --output-spaces argument, where standard and
nonstandard spaces can be inserted.
Important
ASLPrep will reduce the number of output spaces to just spaces listed in --output-spaces,
even if other options require resampling the preprocessed data into intermediary spaces.
Standard spaces
By default, ASLPrep uses MNI152NLin2009cAsym as spatial-standardization reference and
output space. Valid template identifiers can be used from the
TemplateFlow repository.
However, many users will be interested in utilizing a coarse gridding (typically 2 mm isotropic)
of the target template. This can be achieved by applying modifiers to the template identifier,
separated by a : character.
For instance, --output-spaces MNI152NLin6Asym:res-2 will generate
ASL and CBF on standard space (MNI152NLin6Asym) with the template’s 2mm
isotropic resolution.
Nonstandard spaces
Additionally, --output-spaces accepts identifiers of spatial references
that do not generate standardized coordinate spaces:
T1woranat: can be used to resample data into the individual’s anatomical reference (e.g., the T1w image).
func,run,aslorsbrefcan be used to generate ASL/CBF data in their original grid, after slice-timing, head-motion, and susceptibility-distortion corrections as well as CBF computation. These keywords are experimental.
Modifiers are not allowed when providing nonstandard spaces.