LayNii v2.10.0

New programs

• LN2_FRISGO: This program corrects/mitigates the Fuzzy Ripple artifacts in dual polarity 3D-EPI fMRI data.
• LN2_ZSCORE: Simple z-scoring for time series data.
• LN2_DESPIKE: Developed mainly for 3D EPI Dual polarity fMRI data, where moving tissue (e.g. eyeballs) can partially affect the images.
• LN2_RECIPROCAL: Simple reciprocal with a few convenience options.
• LN2_SNAPCAST: Cardinal axis projection for quick surface visuals.

Improvements

We added 64 bit compatibility that is needed to process very large datasets (>5 gb) for the following programs:

• LN2_FRISGO: Completely revised and improved with 64 bit compatibility. Also there is a new -simple flag for the simplest dual polarity correction that developed for dataset with regional spikes (see the new LN2_DESPIKE program).
• LN2_SENSITIVITY: Added 64 bit compatibility.
• LN2_SPECIFICITY: Added 64 bit compatibility.
• LN2_GRAMAG: Added 64 bit compatibility.

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LayNii IDA news

LayNii IDA, our new and fast image viewer GUI is still under work in progress (WIP), however it is coming along nicely. You can find LayNii_IDA executables in separate zip files in the assets section below.

New in LayNii IDA v0.2.0

• Added time index indicator on the time courses. Useful for inspecting spikes.
• Improved automatic contrast handling in in QA controls.
• Added tSNR in QA controls.
• Added tSkewness in QA controls.
• Added tKurtosis in QA controls.
• Added tAutoCorr(temporal auto correlation) in QA controls.
• Added automatic display synchronization across same sized images. This is similar to BrainVoyager's 'link-vmr' and ITKSNAP's 'add additional image' features.
• Real time correlation maps now overlays onto the chosen QA image (e.g. tSNR) rather than being overlayed on the initial data.
• Mask plays along with selected QA image (e.g. tSNR).

LayNii v2.9.0

Improvements

This release provide one major improvement that will propagate to other programs in LayNii over time. We improved an initial handful of programs to be able to handle very large nifti data. These programs for now are:

• LN_BOCO
• LN2_PATCH_FLATTEN
• LN_CORREL2FILES
• LN_TRIAL
• LN_SKEW
  Our main focus was to make them work with FRISGO data that Renzo has been working on.

Experimental

We are introducing LayNii_IDA (LayNii Integrated Discovery/Development Application). LayNii_IDA is a real-time quality assurance and data exploration GUI optimized for very high res. (f)MRI data analysis with extreme speed. We are currently in very early prealpha stage, which means there might be very big and major changes in this software. Therefore, we do not yet advise it to be used for a consistent and stable experience. However, we are excited to share this as a technology demo. The LayNii_IDA executable can be downloaded in addition to the standard LayNii release below.

LayNii v2.8.0

This release features two new and important programs:

• LN2_SENSITIVITY
• LN2_SPECIFICITY

These programs are contributed by #104, and provides voxel-wise computation of the sensitivity and specificity metrics defined in:

• Pizzuti, A., Huber, L. (Renzo), Gulban, O.F., Benitez-Andonegui, A., Peters, J., Goebel, R., 2023. Imaging the columnar functional organization of human area MT+ to axis-of-motion stimuli using VASO at 7 Tesla. Cerebral Cortex 33, 8693–8711. https://doi.org/10.1093/cercor/bhad151

In addition, there are minor improvements in:

• LN2_GEODISTANCE
• LN2_VORONOI

LayNii v2.7.0

Release before OHBM 2024. This release is focused on providing new programs that are focused on computing spatial gradients on magnitude and phase images. These new programs are:

• LN2_GRADIENTS
• LN2_LAPLACIAN
• LN2_GRAMAG
• LN2_PHASE_GRADIENTS
• LN2_PHASE_LAPLACIAN
• LN2_PHASE_JOLT

LayNii v2.6.0

Release after the OHBM abstract deadline. Mainly for start making the new and experimental phase processing tools available to other interested researchers.

New !!! experimental !!! programs

• LN2_PHASE_JOLT: Compute L1 norm of phase image second spatial derivatives.

LayNii v2.5.3

Version 2.5.0 is a relatively minor release before OHBM 2023, introducing the new and major LN2_RIM_POLISH program. As this versions is released shortly after v2.4.0, please also refer to v2.4.0 release notes for other news if you are switching from earlier versions.

New programs

• LN2_RIM_POLISH : Smooth the cortical gray matter borders. Designed to be especially used after manual corrections. Default parameters are optimized for 0.2 mm isotropic images. See this video for an example usage: https://youtu.be/Do77pdTwSy8?t=1124 at around 19:00 . Also see the related issue at: #77

Minor fixes

• [2.5.1] Change programs printing LayNii v2.4.0 to LayNii v2.5.1 upon execution.
• [2.5.2] Add masking options in LN_SKEW and fix several typos in the docstrings.
• [2.5.3] Add safety check for scl slope = 0 in nifti header (see #88 for further details).

LayNii v2.5.2

Version 2.5.0 is a relatively minor release before OHBM 2023, introducing the new and major LN2_RIM_POLISH program. As this versions is released shortly after v2.4.0, please also refer to v2.4.0 release notes for other news if you are switching from earlier versions.

New programs

• LN2_RIM_POLISH : Smooth the cortical gray matter borders. Designed to be especially used after manual corrections. Default parameters are optimized for 0.2 mm isotropic images. See this video for an example usage: https://youtu.be/Do77pdTwSy8?t=1124 at around 19:00 . Also see the related issue at: #77

Minor fixes

• [2.5.1] Change programs printing LayNii v2.4.0 to LayNii v2.5.1 upon execution.
• [2.5.2] Add masking options in LN_SKEW and fix several typos in the docstrings.

LayNii v2.5.1

Version 2.5.0 is a relatively minor release before OHBM 2023, introducing the new and major LN2_RIM_POLISH program. As this versions is released shortly after v2.4.0, please also refer to v2.4.0 release notes for other news if you are switching from earlier versions.

New programs

• LN2_RIM_POLISH : Smooth the cortical gray matter borders. Designed to be especially used after manual corrections. Default parameters are optimized for 0.2 mm isotropic images. See this video for an example usage: https://youtu.be/Do77pdTwSy8?t=1124 at around 19:00 . Also see the related issue at: #77

Minor fixes

• Change programs printing LayNii v2.4.0 to LayNii v2.5.1 upon execution.

LayNii v2.4.0

Modifications

• 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: https://youtu.be/WUgaQBJkRPA14 . #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: https://youtu.be/tIuKG3rtVk4 . #69

Experimental programs and changes

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
• LN2_UVD_FILTER: Add maximum value based depth peak detection -peak_d. We might work on the outputs and change the terminology in the future. #76

LayNii v2.3.0

New programs

New LN2_HEXBIN program is added for generating hexagonal tiling on UVD coordinates.

Modifications

• Docker improvements contributed by @Remi-Gau .
• Citation.cff improvements.
• LN2_PATCH_FLATTEN 4D nifti input and output capability is now added.
• LN2_MULTILATERATE and LN2_PATCH_FLATTEN references are updated to:
  • Gulban, O. F., Bollmann s., Huber L., Wagstyl K., Goebel R., Poser B. A., Kay K., Ivanov D. “Mesoscopic in Vivo Human T2* Dataset Acquired Using Quantitative MRI at 7 Tesla.” NeuroImage 264 (December 2022): 119733. https://doi.org/10.1016/j.neuroimage.2022.119733.