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neuroelf_introduction [2010/06/22 06:41]
jochen created
neuroelf_introduction [2014/06/07 06:09] (current)
jochen updated blurbs about Mac OSX and Octave
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-{{ :neuroelf_facelogo600.jpg?400 |NeuroElf logo }}+{{ http://​neuroelf.net/​face.jpg?400 |NeuroElf logo }}
  
 ====== NeuroElf Introduction ====== ====== NeuroElf Introduction ======
-NeuroElf is a [[http://​www.mathworks.com/​products/​matlab/​|Matlab]]-based toolbox for working with neuro-imaging data. Please be aware that NeuroElf was and is not meant as a replacement ​of any of the more traditional and full-fledged neuro-imaging tools (such as [[http://​www.brainvoyager.com/​products/​brainvoyagerqx.html|BrainVoyager QX]], [[http://​www.fil.ion.ucl.ac.uk/​spm/​software/​spm8/​|SPM]],​ [[http://​afni.nimh.nih.gov/​afni|AFNI]],​ [[http://​www.fmrib.ox.ac.uk/​fsl/​|FSL]],​ [[http://​surfer.nmr.mgh.harvard.edu/​|FreeSurfer]],​ ...), but rather meant to be used in addition to those, as it augments their functionality,​ facilitating ​some of the tasks that might otherwise be more difficult to achieve for those researchers who are not as familiar with coding their own routines in Matlab.+NeuroElf is a [[http://​www.mathworks.com/​products/​matlab/​|Matlab]]-based toolbox for working with neuro-imaging data. Please be aware that NeuroElf was and is not meant as a replacement ​for any of the more traditional and full-fledged neuro-imaging tools (such as [[http://​www.brainvoyager.com/​products/​brainvoyagerqx.html|BrainVoyager QX]], [[http://​www.fil.ion.ucl.ac.uk/​spm/​software/​spm8/​|SPM]],​ [[http://​afni.nimh.nih.gov/​afni|AFNI]],​ [[http://​www.fmrib.ox.ac.uk/​fsl/​|FSL]],​ [[http://​surfer.nmr.mgh.harvard.edu/​|FreeSurfer]],​ ...), but rather meant to be used in addition to those, as it augments ​some of their functionality,​ facilitating ​a few of the tasks that might otherwise be more difficult to achieve for those researchers who are not as familiar with coding their own routines in Matlab.
  
-Core elements of the toolbox ​are a flexible file handling class, **[[xff]]**,​ which gives the user read and write access to the formats used by the above mentioned programs, a GUI element handling class, **[[xfigure]]**,​ that ameliorates some of the issues I encountered while working with Matlab'​s ​uicontrols (such as applying changes to groups of elements and facilitate the somewhat cumbersome access to GUI settings), as well as **[[transimg]]**,​ a class that allows stacking layers of image data for combination to images, and **[[transio]]**,​ an implementation allowing to work with large files without having to read their entire contents into memory.+===== Core elements ===== 
 +Core elements of the toolbox'​s ​functionality are
  
-Additionally, some automatization routines ​(e.g. a small UI for batching preprocessing ​of multiple subjects in SPM5/8), analysis functionality ​(robust regression of second-level neuroimaging data)as well as rudimentary visualization capabilities (display of slice-based overlays ​of statistical results on anatomical ​data) are provided.+  * a flexible file handling class**[[xff]]**,​ which gives the user read and write access to the formats used by the above mentioned programs, and also makes certain "​methods"​ available, with which these objects can be manipulated and the data be made available for various purposes 
 +  * a GUI element handling class, **[[xfigure]]**,​ that ameliorates ​some of the issues I encountered while working with Matlab'​s uicontrols ​(such as applying changes to groups ​of elements and facilitate the somewhat cumbersome access to GUI settings) 
 +  * a configuration file handling class**[[xini]]**,​ allowing to store configuration settings in human readable form (as an alternative to MAT files) 
 +  * as well as **[[transimg]]**,​ a class that allows stacking layers ​of image data for combination to images 
 +  * and **[[transio]]**,​ an implementation allowing to work with large files without having to read their entire contents into memory
  
-To install the toolbox, download from one of the links on the [[http://​neuroelf.net/​|main index page]]. For the first file/​link ​(installerunzip the archivewhich contains two files: NeuroElf_v09b.m ​and NeuroElf_v09b.mat. Open Matlab, change into the folder where you unpacked the archive and enter:+On top of this "​core"​ functionality operates a [[neuroelf_gui|GUI]] that allows the user to access some of the functionality of the core elements via dialogs and formsIn particular it is able to visualize voxel- and surface-based objects, to compute ​(in a limited capacityand display statistical results, and create tables and screenshots of those.
  
-<code matlab>​NeuroElf_v09b -i</​code>​+Another set of features covers the ease by which data can be manipulated,​ but from the command line and the graphical user interface. Particularly the 3D drawing tools have been substantially enhanced in recent releases.
  
-This will ask for target folder and then perform ​the installation.+Additionally,​ some automatization routines (e.g. small UI for batching preprocessing of multiple subjects using the functionality of SPM5/8), analysis functionality (e.g. robust regression of second-level neuroimaging data), as well as some further visualization capabilities (e.g. display of VOI-based averaged trial-locked BOLD responses) are provided.
  
-If, instead, you download the zipped folder or snapshot, please unzip, manually add (without subfolders!) ​to the path, and then enter:+===== Installation ===== 
 +For installation instructionsplease [[NeuroElf installation|read on...]] And you might also want to check out the [[NeuroElf features|list of features]] of the toolbox.
  
-<code matlab>​neuroelf_setup</​code>​+===== Compatibility ===== 
 +Given that Matlab'​s syntax has changed over the years, and some features are not available in very old versions, currently NeuroElf runs (to the best of my knowledge) under the following environments:​
  
-Remember to add the path permanently if you wish to keep NeuroElf available whenever you start up Matlab.+  * Microsoft Windows (tested under Windows XP and Windows 7), using Matlab ​Version v7.5 (R2007b) and onwards 
 +  * Linux (tested under S.u.S.E. Linux 11.2, 64-bit edition as well as Ubuntu 10, 32-bit edition), using Matlab Version v7.5 (R2007b) and onwards 
 +  * Mac OSX (tested under Mac OS 10.7 through Mac OS 10.9), using Matlab Version v7.5 (R2007b) and onwards 
 +  * which beginning with NeuroElf v0.9c there is very basic support for [[http://​www.gnu.org/​software/​octave/​|GNU Octave]]--starting with version v3.4.0--please be aware that I am not regularly testing new functionality against Octave!
neuroelf_introduction.1277181712.txt.gz · Last modified: 2010/06/22 06:41 by jochen