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| neuroelf_installation [2010/06/24 21:16] – created jochen | neuroelf_installation [2011/04/19 02:04] – altered link text to reflect different filename jochen |
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| * whereas many toolboxes require to add several folders to the path, NeuroElf only needs it main folder to be added | * whereas many toolboxes require to add several folders to the path, NeuroElf only needs it main folder to be added |
| * the [[xff]] format files (text files that contain the instructions on how exactly to read/write different file formats) are parsed only once and the result is stored under ''_files/cache/cache.mat''; it is thus important that this folder is writable to the toolbox (particularly when the format files are updated!) | * the [[xff]] format files (text files that contain the instructions on how exactly to read/write different file formats) are parsed only once and the result is stored under ''_files/cache/cache.mat''; it is thus important that this folder is writable to the toolbox (particularly when the format files are updated!) |
| | * additional files can be created by using [[neuroelf_makefiles]] (see its page for settings); but as this might take quite a while to complete with full settings, there is a prepared file for download containing all files: [[http://neureolf.net/NeuroElf_v09c_colin_aux.zip|NeuroElf_v09c_colin_aux.zip]] --after downloading the files from this archive should be unzipped into the ''_files/colin'' subfolder of the installation |
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| | ===== Installation folder structure ===== |
| | Once the toolbox is installed and setup, the following folder structure should be present: |
| | |
| | * **''NeuroElf_vXY''** - root folder containing the functions that are added to the path and are available for scripting |
| | * **''@transimg''** - class directory of the [[transimg]] class that handles blending several RGBA layers to one image |
| | * **''@transio''** - class directory of the [[transio]] class that handles transparent I/O access for large numerical arrays |
| | * ''private'' - transio's privately used functions |
| | * **''@xff''** - class directory of the [[xff]] class that handles complex file/object I/O and method access |
| | * ''private'' - xff's privately used functions (this folder **also contains all objects' method files as type_Method.m files!**) |
| | * **''@xfigure''** - class directory of the [[xfigure]] class that handles additional functionality of Matlab's graphics handles |
| | * **''@xini''** - class directory of the [[xini]] class that handles configuration file I/O and access to settings |
| | * **''@xprogress''** - class directory of the [[xprogress]] class that provides a simplified access to graphics-based progress bars |
| | * **''private''** - this folder contains all functions that are used by the [[neuroelf_gui|GUI]] of NeuroElf |
| | * **''_core''** - this folder contains **required** auxiliary files in sub-folders |
| | * ''config'' - this folder contains the configuration (ini) files read and written to by the [[xini]] class; **this folder must be //writable//!** |
| | * ''dicom'' - this folder contains the (partial) DICOM dictionaries available in NeuroElf |
| | * ''OFFIS'' - this is a copy of an (older) dictionary of the OFFIS DICOM software package |
| | * ''Philips_Achieva'' - this is a (manually edited and partial) dictionary for Philips Achieva DICOM files |
| | * ''Philips_Intera'' - this is a (manually edited and partial) dictionary for Philips Intera DICOM files |
| | * **''formats''** - this folder contains the **BFF** (binary format file) and **TFF** (text format file) specifications that describe how [[xff]] files are read/written |
| | * ''icons'' - this folder contains TIF icons for the [[neuroelf_gui|GUI]] |
| | * ''lut'' - this folder contains the LUT (look-up table) definition files (in BrainVoyager's [[xff - OLT format|OLT format]]) |
| | * ''splash'' - this folder contains the splash images used for the setup routine ([[neuroelf_setup]]) |
| | * ''tfg'' - this folder contains the text-based representation of all complex figures (UI windows) of the toolbox |
| | * **''_files''** - this folder contains **optional** auxiliary files in sub-folders |
| | * ''cache'' - this folder contains the cached version of the ''_files/formats'' files' contents and the methods of all [[xff]] objects; **this folder must be //writable//!** |
| | * ''colin'' - this folder contains the colin_27 template and additional files that can be used to display data that is in MNI/ICBM space (during installation, additional files will be created in this folder!) |
| | * ''compiled'' - this folder (or rather, its subfolders) contain pre-compiled MEX files in case compilation of those files fails during installation |
| | * ''a64'' - compiled MEX files for the A64 (Linux) platform |
| | * ''glx'' - compiled MEX files for the GLX (Linux) platform |
| | * ''mac'' - compiled MEX files for the MAC (PowerPC-Mac) platform |
| | * ''maci'' - compiled MEX files for the MACI (Intel-Mac) platform |
| | * ''maci64'' - compiled MEX files for the MACI64 (64-bit Intel-Mac) platform |
| | * ''w32'' - compiled MEX files for the W32 (32-bit MS Windows) platform |
| | * ''w64'' - compiled MEX files for the W64 (64-bit MS Windows) platform |
| | * ''contrib'' - files that are not part of the main functionality but can potentially be useful for interested users (content not fix between distributions!) |
| | * ''libSVM'' - files bundled as a reference for the libSVM functionality |
| | * ''spm'' - files required for running SPM5/8 based processing steps (e.g. when using [[spm5_preprojobs]] for data preprocessing) |
| | * ''srf'' - additional surface files used for some of the surface-manipulating methods (unit cube, unit cylinder, and unit sphere) |
| | * ''tal'' - files required by the [[tdlocal2]] function for Talairach Demon Database inquiries as well as files for coordinate conversion from TAL to ICBM and vice versa |
| | * ''todo'' - if present (usually SNAPSHOTs only), a collection of files and folders that still require work |
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