====== neuroelf_makefiles ======

===== Motivation =====
To visualize "standard space" (MNI/ICBM space) data with NeuroElf, it is often helpful to have a standardized dataset for underlay (anatomical data and surface files). Instead of bundling these files into the installation (which would require several hundreds of megabytes, even in compressed form), NeuroElf comes with functions to create these files out of a set of source files which come bundled with NeuroElf (and only require about 30 megabytes of uncompressed space). Alternatively, the files created by this function can be downloaded as a [[http://neuroelf.net/NeuroElf_v09c_colin_aux.zip|separate ZIP file]] that needs to be unpacked into the ''_files/colin'' sub-folder.

===== Requirements =====
A functional installation of NeuroElf.

===== Function reference ('help neuroelf_makefiles') =====
<code>   neuroelf_makefiles  - create additional files for NeuroElf's GUI
 
  FORMAT:       neuroelf_makefiles([opts])
 
  Input fields:
 
        opts        optional settings
         .bmaskvmr  also create brain-masked versions of VMRs (true)
         .bvsph     create BV-compatible SPH files of colin (true)
         .flatmaps  create flatmap SRF files (false)
         .hiresseg  create 0.5mm segmentation VMRs of colin brain (false)
         .hiressph  create 0.5mm segmentation-based SPH files (true)
         .hiressrf  create 0.5mm resolution-based SRF files (true)
         .hiressrfb create backprojection VMR files from hires SRFs (false)
         .hiresvmr  create 0.5mm resolution VMR of colin brain (false)
         .icbmimg   also create ICBM-norm version of colin.img (true)
         .icbmsph   also create ICBM-norm versions of SPH files (true)
         .icbmsrf   also create ICBM-norm versions of SRF files (true)
         .icbmvmr   also create ICBM-norm versions of VMR files (true)
         .recreate  delete all files and start anew (false)
         .wmaskvmr  also create (anti-)WM-masked brain VMRs (false)
 
  No output fields.</code>

===== Usage examples =====
To create the files used most, simply call the function without arguments:

  * ''neuroelf_makefiles;''

To create all files, set the flags that default to false to true:

  * ''neuroelf_makefiles(struct('flatmaps', true, 'hiresseg', true, 'hiressrfb', true, 'wmaskvmr', true))'';

==== List of files created ====
All files will be created in the ''_files/colin'' sub-folder.

  * ''**colin_brain.vmr**'' - brain-masked version of the ''colin.vmr'' file (that is created during [[neuroelf_setup]])
  * ''**colin_brain_ICBMnorm.vmr**'' - ICBM (segmentation-based) normalized version of ''colin_brain.vmr'' (useful if functional/statistical data comes from a project for which SPM's segmentation was used as normalization procedure)
  * ''colin_brain_WMmasked.vmr'' - brain-masked version that also has white matter masked out (useful for masking data files; only created if the '''.wmaskvmr''' flag is set to ''true'')
  * ''colin_hires.vmr'' - 0.5mm resolution VMR, created using lanczos/windowed-sinc interpolation (for high-quality renderings)
  * ''colin_hires_brain.vmr'' - 0.5mm resolution VMR, brain-masked, created using lanczos/windowed-sinc interpolation (for high-quality renderings)
  * ''colin_hires_ICBMnorm.vmr'' - 0.5mm resolution VMR, created using lanczos/windowed-sinc interpolation (for high-quality renderings)
  * ''colin_hires_brain_ICBMnorm.vmr'' - 0.5mm resolution VMR, brain-masked, created using lanczos/windowed-sinc interpolation (for high-quality renderings)
  * ''colin_ICBMnorm.hdr'' and ''colin_ICBMnorm.img'' - ICBM (segmentation-based) normalized version of ''colin.img'' (the file that comes bundled with NeuroElf)
  * ''colin_LH_SPH.srf'' and ''colin_RH_SPH.srf'' - legacy surface file for the left and right hemispheres (LH/RH, 40962-vertex, morphed icosahedron meshes)
  * ''colin_LH_SPH_ICBMnorm.srf'' and ''colin_RH_SPH_ICBMnorm.srf'' - ICBM-normalized versions of the ''colin_LH_SPH.srf'' and ''colin_RH_SPH.srf'' files
  * ''colin_hires_LH_seg.vmr'' and ''colin_hires_RH_seg.vmr'' - 0.5mm-resolution segmentation (white matter) of left and right hemispheres
  * ''**colin_hires_LH_seg_RECOSM.srf**'' and ''**colin_hires_RH_seg_RECOSM.srf**'' - high-resolution (600k+ vertices) meshes of left and right hemisphere
  * ''**colin_hires_LH_seg_RECOSM_ICBMnorm.srf**'' and ''**colin_hires_RH_seg_RECOSM_ICBMnorm.srf**'' - ICBM-normalized versions of these files
  * ''colin_hires_BH_segback.vmr'', ''colin_hires_LH_segback.vmr'', and ''colin_hires_BH_segback.vmr'' - 0.5mm-resolution back-projection of surfaces (for rendering)
  * ''colin_hires_BH_segback_ICBMnorm.vmr'', ''colin_hires_LH_segback_ICBMnorm.vmr'', and ''colin_hires_RH_segback_ICBMnorm.vmr'' - ICBM-normalized versions of these files
  * ''colin_hires_LH_seg_FLAT.srf'' and ''colin_hires_RH_seg_FLAT.srf'' - flattened surface of the hi-resolution RECOSM files (for flat maps)
  * all ''*_hires_*_SPH160k.srf'' files - hi-resolution mesh/surface files resampled at regular intervals along a morphed 163842-vertex icosahedron mesh
  * all ''*_midres_*_SPH40k.srf'' files - mid-resolution mesh/surface files resampled at regular intervals along a morphed 40962-vertex icosahedron mesh
  * all ''*_lowres_*_SPH10k.srf'' files - low-resolution mesh/surface files resampled at regular intervals along a morphed 10242-vertex icosahedron mesh