Index to shell scripts

• scripts to calculate means
  
  • base_norm -- normalizes time-series data to a base scan (must be first scan in set).
  • convert_means -- takes a 5-column time-series file as input and produces output in the same format except that activations are given as percent difference from the mean.
  • scan_means -- takes a time-series file as input and computes mean activations for each image.
  • get_roi_means2 -- takes a design file and a time-series file as input and produces a table of mean activations by factors. Note: you must customize this script for your experiment.
  • get_normed_roi_means -- takes a timeseries file and design file as input, outputs means for each ROI expressed as percent signal change relative to scan 1 in a trial. Note: you must customize this script for your experiment.

• conversion scripts
  
  • air2pgh1.csh -- utility to convert files from ANALYZE format to pgh1 format.
  • decompress.csh -- utility to uncompress directory contents.
  • nih2an -- converts a Macintosh NIH Image file into ANALYZE format.
  • nisepi2an.pl -- converts EPI format files into ANALYZE format.
  • make_analyze -- converts structural image files from raw GE format to ANALYZE format. make_analyze help
  • pgh2air.csh -- utility to convert files from pgh1 format to ANALYZE format.
  • rename -- renames multiple files simultaneously based on a given regular expression.

• make_design -- takes a PsyScope output file and subject name (e.g., wg304) as input. Produces a trial-based ascii design file that can be used as input to nisanova in a event-related experiment. Note: you must customize this script for your experiment, several sample scripts are included:
  • make_design.axd (CPT-AX)
  • make_design.nb (N-back)
• do_everything -- prepares individual subject data for group analysis by invoking the following scripts. Note: these scripts call AIR routines.
  • do_xreg -- align each subject's structural to standard structural, shrink it, do a few more somersaults, end up with AIR matrices for aligning functionals.
  • do_reslice -- reslice each subject's functionals to align with standard.
  • do_norm -- normalize resliced functionals
  • do_smooth -- smooth normalized functionals
  • do_params1 -- parameters for reslice command in do_xreg
  • do_params2 -- parameters for reslice command in do_xreg