From 5469692c1296e6696d7a7e2c23244f8d8b0867c7 Mon Sep 17 00:00:00 2001 From: Rudolph Pienaar Date: Fri, 5 Feb 2021 15:06:23 -0500 Subject: [PATCH] Minor updates and bump to 2.0.8 --- README.rst | 14 +++++++------- mgz2imageslices/mgz2imageslices.py | 2 +- setup.py | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/README.rst b/README.rst index e71046a..ab364fc 100644 --- a/README.rst +++ b/README.rst @@ -46,7 +46,7 @@ Synopsis [--version] \ [-y] [--synopsis] \ \ - + Description ----------- @@ -55,7 +55,7 @@ Description For more detailed description, consult the documentation here https://github.com/FNNDSC/mgz2imgslices -**NOTE:** +**NOTE:** In the instances where the input ``mgz`` volume voxel values are interpreted to imply *labels* (i.e. segmented cortical regions), this plugin can use the embedded FreeSurfer ``FreeSurferColorLUT.txt`` file to map FreeSurfer *label* IDs to human readable cortical label strings in the naming of output directories. @@ -107,13 +107,13 @@ Arguments the to ``__val__``. While running the docker image, you can also pass ``__fs__`` which will use - the FreeSurferColorLUT.txt from within the docker container to perform a - looktup on the filtered voxel label values according to the contents of + the FreeSurferColorLUT.txt from within the docker container to perform a + looktup on the filtered voxel label values according to the contents of the FreeSurferColorLUT.txt [--skipAllLabels] Skips all labels and converts only the whole mgz volume to png/jpg images. - + [-s|--skipLabelValueList ] If specified as a comma separated string of label numbers, will not create directories of those label numbers. @@ -179,7 +179,7 @@ First, let's create a directory, say ``devel`` wherever you feel like it. We wil cd devel export DEVEL=$(pwd) -Now, we need to fetch sample MGZ data. +Now, we need to fetch sample MGZ data. Pull MGZ data ~~~~~~~~~~~~~ @@ -232,7 +232,7 @@ Copy and modify the different commands below as needed: --skipLabelValueList 0,2 \ --normalize \ --saveImages \ - --wholeVolume entireVolume \ + --wholeVolume entireVolume \ --verbosity 1 \ /incoming /outgoing diff --git a/mgz2imageslices/mgz2imageslices.py b/mgz2imageslices/mgz2imageslices.py index aa75676..6654ea4 100755 --- a/mgz2imageslices/mgz2imageslices.py +++ b/mgz2imageslices/mgz2imageslices.py @@ -58,7 +58,7 @@ class Mgz2imgslices(ChrisApp): TYPE = 'ds' DESCRIPTION = 'An app to convert mgz volumes to numpy arrays and png image formats' DOCUMENTATION = 'https://github.com/FNNDSC/pl-mgz2imgslices' - VERSION = '2.0.6' + VERSION = '2.0.8' ICON = '' # url of an icon image LICENSE = 'Opensource (MIT)' MAX_NUMBER_OF_WORKERS = 1 # Override with integer value diff --git a/setup.py b/setup.py index 452203f..126f0ad 100755 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ def readme(): name = 'mgz2imgslices', # for best practices make this version the same as the VERSION class variable # defined in your ChrisApp-derived Python class - version = '2.0.6', + version = '2.0.8', description = 'An app to ...', long_description = readme(), author = 'FNNDSC',