cmind.finders

Utilities to find various external packages

Functions

check_exist(progs) utility to check existance of various external programs
find_AFNI() Find AFNI binary folder by checking the following locations:
find_ANTS() Find ANTs by checking the following locations:
find_DTIPrep() Find DTIPrep binary by checking the following locations:
find_FSL() locate FSL via FSLDIR environment variable and determine its version
find_GraphicsMagick() Find GraphicsMagick by checking the following locations:
find_ImageMagick() Find ImageMagick by checking the following locations:
find_MNI_templates([cmind_FSL_dir]) Find MNI standard brains via searching in the following locations
find_Slicer3D()
find_shellscripts() Find the cmind shell scripts such as transpose_dirs.sh
get_Slicer3D_version(Slicer3D) Find 3D Slicer version information
cmind.finders.check_exist(progs)[source]

utility to check existance of various external programs

Parameters:

progs : str or list of str

list of programs to find (case insensitive)

Notes

Can check for the following programs: FSL, ANTs, AFNI, DTIPrep, MNI Templates, 3DSlicer, ImageMagick

cmind.finders.find_AFNI()[source]
Find AFNI binary folder by checking the following locations:
  1. environment variable AFNIPATH
  2. searching for afni on the path
Returns:

AFNI_dir : dir

directory containing the AFNI binaries

AFNI_version_info : str

AFNI version number

cmind.finders.find_ANTS()[source]
Find ANTs by checking the following locations:
  1. environment variable ANTSPATH
  2. searching for antsRegistration on the path
Returns:

ANTs_dir : dir

directory containing the ANTs binaries

cmind.finders.find_DTIPrep()[source]
Find DTIPrep binary by checking the following locations:
  1. environment variable DTIPREP
  2. searching for DTIPrep on the path
Returns:

DTIPrep : file

filename of the DTIPrep binary

DTIPrep_version : str

DTIPrep version number

cmind.finders.find_FSL()[source]

locate FSL via FSLDIR environment variable and determine its version

Returns:

FSL_dir : $FSLDIR

fsl_version : FSL version number

cmind.finders.find_GraphicsMagick()[source]
Find GraphicsMagick by checking the following locations:
  1. searching for gm on the path
Returns:

has_GraphicsMagick : bool

True if ImageMagick was found

GraphicsMagick_version_info : str

GraphicsMagick version information

cmind.finders.find_ImageMagick()[source]
Find ImageMagick by checking the following locations:
  1. searching for convert on the path
Returns:

has_ImageMagick : bool

True if ImageMagick was found

ImageMagick_version_info : str

ImageMagick version information

cmind.finders.find_MNI_templates(cmind_FSL_dir=None)[source]
Find MNI standard brains via searching in the following locations
  1. environment variable MNIDIR
  2. if FSL is installed, try $FSLDIR/data/standard
Returns:

cmind_MNI_dir : dir

directory containing the MNI standard brains

cmind.finders.find_Slicer3D()[source]
cmind.finders.find_shellscripts()[source]

Find the cmind shell scripts such as transpose_dirs.sh

cmind.finders.get_Slicer3D_version(Slicer3D)[source]

Find 3D Slicer version information

Returns:

Slicer3D_version : str

3D Slicer version number