updating documentation part 2

README.md

@@ -1,28 +1,12 @@
 
-# ----- Allen ROI Extraction ----- #
-The VBM pipeline generates images in which maximum change has been observed in specific brain regions across a group of subjects. These images are referred to as cluster images here, that will be used by the Allen ROI Extraction tool.
-The toolbox has two functionalities - creation of masks of user-specified brain regions (ROIs) and specifying the proportion of brain regions in cluster images, obtained from VBM analysis.
-
-# ----- Getting Started ----- # (also provided in manual)
+# ----- Allen ROI Extraction Toolbox ----- #
+The VBM pipeline in SPM generates images in which maximum change has been observed in specific brain regions across a group of subjects. These images are referred to as cluster images here, that are used by the Allen ROI Extraction toolbox.
+The toolbox has two functionalities - ROI Extraction and Cluster Labelling. ROI Extraction involves creation of masks of user-specified brain regions (ROIs) and, Cluster Labelling involves specifying the proportion of brain regions in cluster images, obtained from VBM analysis.
 
 # Download and Installation #
-1. Download and install SPM and add it to your Matlab search path.
-2. Download the Allen ROI Extraction tool from the following link: git@github.molgen.mpg.de:chaudhuri/Allen_ROI_Extraction.git
-3. Copy the toolbox to a preferred location in your file system.
-4. Add fullpath of the toolbox to Matlab.
-
-# Using the functionalities: how to run the scripts #
-1. Creation of masks of ROIs
-
-a) Change working directory to the Allen ROI Extraction tool and run the script titled
-   ‘annotation_tan'.
-b) 'DataDir' is the fullpath to the folder which contains the cluster images. Enter that as a string as the script is executed.
-c) ‘TemplatesDir' is the fullpath to the folder which contains the ROI templates in the desired resolution. Enter that as a string as the script is executed.
-d) ‘brain_region’ is the brain region in the whose the mask the user wishes to generate. Enter the name of the brain region exactly how it is labelled in the Allen brain reference atlas. Check this link http://atlas.brain-map.org/atlas?atlas=1&plate=100960336#atlas=1&plate=100960432&resolution=16.75&x=4655.875&y=3511.875&zoom=-3&structure=68 to see how they have been labelled.
-
-2. Specifying proportion of brain regions in cluster images
+1. This toolbox has been tested on Matlab R2019a.
+2. This toolbox has been tested on SPM12 version 7771. Download and install SPM12 and add it to your Matlab search path using the addpath(genpath()) command from Matlab. SPM can be downloaded from the following link: https://www.fil.ion.ucl.ac.uk/spm/software/download/.
+3. Download the Allen ROI Extraction Tool(ARET) from the following link: https://github.molgen.mpg.de/chaudhuri/ARET.git. Copy the toolbox to a preferred location in your file system and add its path to Matlab, using addpath(genpath) command from Matlab. This can be done in the following way - addpath(genpath(‘*fullpath to ARET in your filesystem*’)).
 
-a) Change working directory to the Allen ROI Extraction tool and run the script titled 'Cluster_Overlap_main'.
-b) 'CodeDir' is the fullpath to the Allen ROI Extraction tool. Enter that as a string as the script is executed.
-c) 'DataDir' is the fullpath to the folder which contains the cluster images. Enter that as a string as the script is executed.
-d) The prefix of the filenames of the cluster images is the first letter of the filename followed by '_' character. Hence, if the filename starts with 'W' character, the prefix to be entered during script execution is 'W_'.
+# Contact Information #
+For further information and clarification about ARET please contact Tanusree Chaudhuri <tanusree_chaudhuri@psych.mpg.de> or Michael Czisch <czisch@psych.mpg.de> of Max Planck Institute of Psychiatry, Munich.