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 separate ZIP file that needs to be unpacked into the _files/colin sub-folder.

A functional installation of NeuroElf.

   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.

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));

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