Releases: layerfMRI/LAYNII
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_BOCOLN2_PATCH_FLATTENLN_CORREL2FILESLN_TRIALLN_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_SENSITIVITYLN2_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_GEODISTANCELN2_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_GRADIENTSLN2_LAPLACIANLN2_GRAMAGLN2_PHASE_GRADIENTSLN2_PHASE_LAPLACIANLN2_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 v2.4.0toLayNii v2.5.1upon execution. - [2.5.2] Add masking options in
LN_SKEWand fix several typos in the docstrings. - [2.5.3] Add safety check for
scl slope = 0in 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 v2.4.0toLayNii v2.5.1upon execution. - [2.5.2] Add masking options in
LN_SKEWand 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 v2.4.0toLayNii v2.5.1upon execution.
LayNii v2.4.0
Modifications
LN2_MULTILATERATE: Speed up perimeter update. #75LN2_VORONOI: Add maximum distance parameter (useful for very large files e.g. 0.1 mm whole brain). #75LN2_COLUMNSandLN2_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 . #71LN2_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 usingcircularflag. #65LN2_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. #66LN2_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.cffimprovements.LN2_PATCH_FLATTEN4D nifti input and output capability is now added.LN2_MULTILATERATEandLN2_PATCH_FLATTENreferences 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.
Contributors
Assets 5
LayNii v2.2.1
Purpose of the release
LN2_MULTILATERATE and LN2_PATCH_FLATTEN focused release to serve as a checkpoint for:
- Gulban, O. F., Bollmann, S., Huber, R., Wagstyl, K., Goebel, R., Poser, B. A., Kay, K., Ivanov, D. (2021). Mesoscopic Quantification of Cortical Architecture in the Living Human Brain. BioRxiv. https://doi.org/10.1101/2021.11.25.470023
Modifications
LN2_LAYERSnow outputs approximately equal number of voxels for each layer with-equal_countsflag. This option can be useful for low resolution inputs (e.g. > 0.5 mm iso.). Note: when activating this flag, it will equalize the number of voxels for each layer without respecting equi-distant and equi-volume cortical depth measurements.LN_RAGRUGnow has-scaleparameter to create rectangular tessellations at lower resolutions (integer multiples of the input voxel dimensions.- Binaries for MACOS M1 chip will be included from now on.
- [v2.2.1] Minor fixes to outputs of
LN2_MULTILATERATEand help menu improvements.