Within fastmap, use “help” —> “startup options” to see all current options.
Usage: fastmap [options] [file1] [file2] ...
Files are NIFTI (.nii or .nii.gz) or JIP format (binary file with separate header).
Without modifiers, files are placed into the time-series space. Other input files can be referenced with these options:
-T, --template-directory [directory name] for anatomy/atlas/overlays
-a, —anatomy [file name] Open anatomy file (different space from time-series)
-A, —atlas [file name] Open atlas and label files (anatomy space)
-c, —color [file name] Open color file using linear scale
-P, —PValue [file name] Open file containing log-10 numbers, with sign giving tail
-o, --overlay-list [file name] Open a list of overlays
-I, --alignment-file [file name] Read an alignment file
-t, --time-model [file name] Open a time model file, including time-series files
Batch and convenience options:
--output-file [file name] Define an output file name (names are memorized)
--calibrate [region name] find k2’ for SRTM3—>SRTM2 (region from overlay list)
-f, --fastmap-input Read command line AND fastmap file options on current directory
—smoothing [FWHM of smoothing kernel]; this information is memorized
-O, —open [name] Open time model or pre-processing page (see names below)
--preprocess [name] Apply a preprocessing option (names below)
-q, --quit Quit after running
-b, --batch Suppress GUI
-M, --map Calculate maps from time model
Rarely used options, due to memorized settings that span sessions:
—threads [# of threads] to specify number of threads for processing
-1, --1-slice Use 1 display panel
-3, --3-panels Use 3 orthogonal panels
--all, --all-slices Use full mosaic
-m, --mosaic Use partial mosaic
-Y, --flip-up-down Mirror images in y
-y, --do-not-flip Do not mirror images in y
-p, --percent Use percent units.
-h, --help Displays help; also available from menu “help” —> “startup options”
Preprocessing names: smooth, clip, reslice, asl, pvc, align, register, register-overlays-forward
Time model names: fmri, pet-rtm, mem, adc, dti, t1, t2