LayNii v2.1.0

New programs

LN2_GEODISTANCES to measure geodesic distances in a set of voxels from another set of voxels.
LN2_IFPOINTS is a simplified (and more general) version of the iterative farthest points algorithm used in LN2_COLUMNS.
LN2_MASK is intended to help with voxel section for layer-profile extraction.
LN2_BORDERIZE is introduced to find borders in an integer nifti (e.g. segmentation files, rim files).

Modifications

LN2_MULTILATERATE algorithm is significantly improved through using pin axis geodesic distances rather than point based geodesic distances.
LN2_LAYERS now have a very minimal masked smoothing applied to the equivolume and equidistance metrics. This is done to mitigate the discrete sampling effects present close to the borders.

LayNii v2.0.0

Added programs:

• LN2_CONNECTED_CLUSTERS to remove islands of unconnected voxels
• LN2_MULTILATERATE to obtain rectangular grid in convoluted cortex
• LN2_PATCH_FLATTEN to re-map topographical signal distributions of convoluted cortex in 3D nii
• LN2_CHOLMO to add additional layers on already existing ones (padding)
• LN2_PROFILE to extract layer-profiles from any activity map based on layer masks
• LN_CONLAY to reduce the layer grid to match native resolution of functional data (for Fede).

Added features

• New contributions about default output paths in LN_BOCO by alepizzuti
• Orientation to main magnetic field added in LN2_LAYERS
• LN2_LAYERS has a new -incl_borders option to extend layer profiles
• Improved thickness estimation in LN2_LAYERS
• Added additional references in the source file of LN2_DEVEIN, as per reviewers request
• Programs with LN2 prefix have been vetted more thoroughly and are no longer experimental.
• Unused and too experimental programs are archived.

LayNii v1.6.0

Improvements

• Consistency issues in LN2_DEVEIN are addressed (see the discussion at #28 ).
• NOTE: Binaries will be added in a later minor release. If you are not planning to use LN2_DEVEIN or LN2_COLUMNS you do not need to update LAYNII.

New features

• Introducing LN2_COLUMNS program. This program implements a very simple method to generate approximately equal volume columns in 2D and 3D images. This program uses middle gray matter (midgm) output of LN2_LAYERS and is designed to be used in combination.
• New programs with LN2 prefix are mostly experimental. Therefore, use these programs by knowing that they might be subject to extensive changes until LAYNII v2.0.0.

LayNii v1.5.6

Improvements

• All programs now can handle absolute and relative input paths and save outputs in the input folder.
• Input data type casts are tightened for all programs. This addresses many issues stemming from various integer data types (int8, int16, int32 etc.)
• NaNs in input images are swapped with zeros. Addressing many issues coming from NaN voxels.
• Lots of under the hood improvements and restructuring laying the groundwork for future additions.
• [1.5.1] Introducing custom output path in LN_BOCO, LN_MP2RAGE_DNOISE, LN_FLOAT_ME, LN_SHORT_ME, LN_INT_ME. This flag will also be added to other programs as needed in the future.
• [1.5.1] Fixing minor bugs introduced in 1.5.0 after restructuring.
• [1.5.2] Added support for .nii.gz read/write.
• [1.5.3] Fix displayed version number in welcome message.
• [1.5.4] Add rim_M.nii as a synthetic 2D test image.
• [1.5.5] Add equi-distant and equi-volume metrics as additional default outputs to LN2_LAYERS.
• [1.5.6] Outputs are now changed to use suffix tags instead of prefix in ALL programs.
• [1.5.6] Nii.gz bug fix for windows
• [1.5.6] The testing files and scripts are updated to match the new options after v1.5
• [1.5.6] LN_GRADSMOOTH_ITER is added to avoid signal smoothing across kissing gyri.
• [1.5.6] binaries are added
• [1.5.6] binaries for Windows x64 added

New features

• Introducing LN2_LAYERS program. This program implements a vastly faster equidistant layering algorithm suitable for generating layers in very large images. Also comes with middle gray matter, thickness and approximate curvature outputs.
• New programs with LN2 prefix are mostly experimental. Therefore, use these programs by knowing that they might be subject to extensive changes until LAYNII v2.0.0.

LayNii v1.0.0 (legacy)

We are keeping this pre-2020 version around in case if someone was already using it. However, it is highly recommended to use a newer version of LAYNII.