Command-line Utilities
Some features of the application can be made available at the command-line. The easiest way to set this up is to run the Install Utilities tool, which can be found in the Options menu of the application toolbox.
The following utilities are currently available. Once installed, run at the command-line with no arguments to see parameters usage.
mango
Mango image loader (v3.5 b-1344) Usage: mango [-q] [-r] <file> [-o] [overlay file] Options: -r reload this image -o overlay this image on previous image -q quit application -k quit application immediately
mango-applytransform
Applies transform to image (v3.5 b-1344) Usage: applytransform [-c | -o] <matrix file> <image file> [output file] Usage: applytransform -d <matrix file> Options: -c apply as world transform (about image center) -o apply as world transform (about image origin) -d decompose transform
mango-convert2avw
Converts recognized file formats to AVW format (v3.5 b-1344) Usage: convert2avw [-a] [-out file] <files> Options: -a anonymize metadata -out specify output file
mango-convert2des
Converts recognized file formats to DES format (v3.5 b-1344) Usage: convert2des [-a] [-s] [-out file] <files> Options: -a anonymize metadata -out specify output file
mango-convert2nii
Converts recognized file formats to NIFTI format (v3.5 b-1344) Usage: convert2nii [-a] [-s] [-out file] <files> Options: -a anonymize metadata -2 output in NIFTI-2 format -out specify output file
mango-imageinfo
Prints a summary of image metadata (v3.5 b-1344) Usage: imageinfo [-f] <header> Option: -f print full header
mango-makeroi
Makes a ROI based on image threshold (v3.5 b-1344) Usage (simple threshold): makeroi [-min <value>] <files> Usage (shrink wrap): makeroi -s [-axi | -cor | -sag | -3d] [-min <value>] <files> Usage (convex hull): makeroi -c [-min <value>] <files> Options: -min lower threshold (default: based on display range) -max upper threshold -0 exclude zero -s shrink wrap -c convex hull -axi, -cor, -sag, -3d shrink wrap direction (default: axi) -color use ROI color 0 - 7 (default: 0) -label add a label for this ROI color
mango-resizer
Resize image (v3.5 b-1344) Usage: resizer [-q] [-r] <file> [-o] [overlay file] Options: -r reload this image -o overlay this image on previous image -q quit application -k quit application immediately Note: To use the currently open instance, open Mango preferences, enable the 'Command Line' option, save changes, and restart Mango. michaels-pro:Desktop michaelmartinez$ mango-resizer Resizes an image voxel array (v3.5 b-1344) Usage: resizer <infile> <xImageDim> <yImageDim> <zImageDim> <outfile> Usage: resizer <infile> -reslice <xImageDim> <yImageDim> <zImageDim> <xVoxelDim> <yVoxelDim> <zVoxelDim> <outfile> Usage: resizer <infile> <xLeft> <xRight> <yPos> <yAnt> <zInf> <zSup> <outfile> Options: <xDim> <yDim> <zDim> the desired output extent of each dimension (changes are symmetrical) -reslice <xImageDim> <yImageDim> <zImageDim> <xVoxelDim> <yVoxelDim> <zVoxelDim> the desired output image and voxel dimensions <xLeft> <xRight> <yPos> <yAnt> <zInf> <zSup> amount to add or subtract from each edge of image
mango-script
Runs a Mango script (v3.8 b-1460) Usage: script [-f][-o file] [-p file] [-r file] [-s file] [-a atlas] [-out file] [-b] Usage: script [-e] [-o file] [-p file] [-r file] [-s file] [-a atlas] [-out file] [-b] Option: -f script file Option: -e1 image calculator expression, all voxels (e.g., "this+1") Option: -e2 image calculator expression, inside ROI (e.g., "this+1") Option: -e3 image calculator expression, outside ROI (e.g., "this+1") Option: -o overlay file Option: -p parametric overlay file Option: -r roi file Option: -s surface file Option: -a atlas name Option: -out output file name Option: -b batch mode (script is run on each individually loaded volume manager) Example: script "My Script" myFile -o myFileOvly myFile2 -o myFile2Ovly Example: script -f myScript.py myFile
mango-vols2series
Concatenate volumes into a series (v3.5 b-1344) Usage: vols2series [-f] [-u | -m | -s <time>] -out <output> <files> Options: -f force output image to be floating-point -u microseconds -m milliseconds -s seconds -out specify output file