REX Region of interest EXtraction toolbox
Extracts values from the selected NIFTI data files at the specified Regions of Interest (ROIs)
Developed by Alfonso Nieto-Castanon
This software has now been integrated with and is being further developed as part of CONN
Installation
This software requires SPM (SPM - http://www.fil.ion.ucl.ac.uk/spm/)
After downloading this software simply prepend the rex directory to your MATLAB path to complete the installation.
Usage
rex;
Launches interactive GUI
MEANS=rex(SOURCES, ROIS);
where SOURCES is a list of M source volume files (image files to extract from)
and ROIS is list of N roi files (image or .tal files)
returns the mean values of each of the source volume files at the voxels
identified by each ROI in the matrix MEANS (with size M x N).
rex(SOURCES, ROIS, 'paramname1',paramvalue1,'paramname2',paramvalue2,...);
permits the specification of additional parameters:
'summary_measure' : choice of summary measure (across voxels) [{'mean'},'eigenvariate','weighted mean','weighted eigenvariate','median','sum','weighted sum','count','max',min']
'level' : summarize across [{'rois'},'clusters','peaks','voxels']
'scaling' : type of scaling (for timeseries extraction) [{'none'},'global','roi']
'conjunction_mask': filename of conjunction mask volume(s)
'conjunction_threshold' absolute-threshold defining voxels within conjunction_mask [0] (e.g. conjunction_threshold=0 or conjunction_threshold={'raw', 0} keeps all voxels with mask values above zero within each ROI; conjunction_threshold={'voxels', 10} keeps only the 10 voxels with the highest values in the conjunction mask within each ROI; conjunction_threshold={'percent', .10} keeps only voxels with top 10% values in the conjunction mask within each ROI
'output_type' : choice of saving output ['none','save','savefiles',{'saverex'}]
'gui' : starts the gui [{0},1]
'disregard_zeros' when datatype has no NaN representation treat 0 as NaN [0,{1}]
'roi_threshold' absolute-threshold defining voxels within cluster [0]
'select_clusters' asks user to select one or more clusters if multiple clusters exists within each ROI [{0},1]
'selected_clusters' (for 'select_clusters'=0) indexes of clusters to select (by default this value is empty and all of the clusters will be selected)
'dims' : (for 'eigenvariate' summary measure only): number of eigenvariates to extract from the data
'covariates' : (for 'eigenvariate' summary measure only): covariates to be regressed-out before computing svd
'pca' : (for 'eigenvariate' summary measure only): PCA decomposition 1 = first extract component represents mean signal, next components represent principal component decomposition of covariance matrix); 0 = components represent SVD decomposition of the second moment (X'*X) matrix [0,{1}]
'mindist' : (for 'peak' level only): minimum distance (mm) between peaks
'maxpeak' : (for 'peak' level only): maximum number of peaks per cluster
'fsanatomical' : (for ROIs defined on freesurfer cortical surfaces): subject-specific freesurfer-generated mri/T1.nii structural file
'output_files': (for output_type 'save' or 'savefiles' only): cell array of files to create {'data.txt','data.mat','roi.tal','roi.img','roi#.img'}
other command-line usages:
rex open : opens existing rex.mat file