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LayNii: A software suite for layer-fMRI

Huber, Laurentius; Benedikt, Poser; Bandettini, Peter; Arora, Kabir; Wagstyl, Konrad; Cho, Shinho; Goense, Jozien; Nothnagel, Nils; Morgan, Andrew Tyler; van den Hurk, Job; Müller, Anna Katharina; Reynolds, Richard; Glen, Daniel; Goebel, Rainer; Gulban, Omer Faruk

  • LN2_MULTILATERATE: Speed up perimeter update. #75
  • LN2_VORONOI: Add maximum distance parameter (useful for very large files e.g. 0.1 mm whole brain). #75
  • LN2_COLUMNS and LN2_IFPOINTS: Now prints the maximum distance between centroids/points. Useful for understanding the approximately average distance between centroids/points. #70
New programs
  • LN2_PATCH_FLATTEN_2D : For flattening 2D slices (e.g. histology data). See this video for usage: . #71
  • LN2_PATCH_UNFLATTEN: Unflattening for 3D flattened files (e.g. vitual Petri dishes, cakes ...). See the last 15 minutes of this video for and example usage: . #69
Experimental programs

There are the new programs which might be modified without concerning backwards compatibility. They are highlighted in the makefile and will be removed from that section once stabilized.

  • LN2_GRAMAG: Compute gradient magnitude images. Can compute phase image gradient magnitudes correctly when using circular flag. #65
  • LN2_NEIGHBORS: Find 1st order neighbors of an any given input containing integers (segmentations, parcellations, custom regions of interests etc.). This program yields a comma spearated values file (.CSV) as the default output. In the future we might make use of such neighborhood information files in LayNii. #66
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