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 2mm 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:

  • T1w or anat: can be used to resample data into the individual’s anatomical reference (e.g., the T1w image).
  • func,``run``, asl or sbref can 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.