Fastmap assumes a typical and common-sense organization in which each “run” or “scan” is contained in a different directory. It is very common in imaging by MRI, PET, and other modalities to preprocess data: e,g,, raw data is transformed by correcting for motion, smoothing, spatially normalized to a standard space, etc. Therefore, it’s common to adopt file naming conventions that match the preprocessing steps. For instance, one might start with 4D files named “raw.nii” in each of several fMRI scan directories. Correction for motion would create a series of corresponding files named “mc.nii” in each of the scan directories, and so on.
Fastmap preprocessing modules provide modifiable output file names (e.g., “smooth”) with the intention of saving one such file into all of multiple input directories. Smoothing of 15 fMRI input files named “raw.nii” in 15 different directories will lead to 15 output files named (e.g.) “smooth.nii”, with one such file in each of the 15 input directories. Therefore, an organization of one directory per “scan” is encouraged: