Owner
khanlab
30 indexed repositories · View on GitHub
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hippunfold
BIDS App for Hippunfold (automated hippocampal unfolding and subfield segmentation)
Python · 69 stars
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snakebids
Snakemake + BIDS
Python · 23 stars
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zarrnii
Package for working with OME-Zarr and NIFTI images in a unified manner, with a focus on spatial transformations
Python · 11 stars
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Python · 9 stars
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SPIMquant
SnakeBIDS app for quantitative analysis of SPIM (lightsheet) brain data
Python · 8 stars
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scattr
BIDS app for structural connectivity between targeted regions
Python · 7 stars
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labelmerge
Merge label maps
Python · 6 stars
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SPIMprep
A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
Python · 6 stars
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kslurm
Helper scripts and wrappers for running commands on SLURM compute clusters.
Python · 5 stars
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neuroglia-helpers
Helper and wrapper scripts for using Singularity locally and on compute canada
Shell · 5 stars
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prepdwi
BIDS-app for pre-processing DWI (denoise, unring, top-up, eddy, bedpost.. )
MATLAB · 3 stars
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mp2rage_correction
BIDS App for correction of residual B1 in MP2RAGE based on Sa2RAGE (code from JP Marques)
MATLAB · 3 stars
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hippunfold-atlases
Surface-based atlases for hippunfold v2.x
3 stars
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cfmm2bids
Snakemake workflow for pulling cfmm dicom server data into bids
Python · 3 stars
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hippunfold-templateflow
Hippunfold outputs on templateflow templates
2 stars
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funcmasker-flex
BIDS App for U-net brain masking of fetal bold MRI
Jupyter Notebook · 2 stars
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Perl · 2 stars
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gradcorrect
BIDS app for correcting gradient non-linearities, saves corrected images as mirrored BIDS dataset, along with warp and intensity-correcti...
Shell · 2 stars
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khanlab.github.io
Khan Lab website
HTML · 2 stars
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hippunfold-plot
Plotting functions for hippocampal surface maps from HippUnfold
Jupyter Notebook · 1 star
- 10 more repositories live on View on GitHub
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khanlab/template-circleci#2 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/template-circleci#3 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/neuroglia-core#1 · 0 comments · 0 reactions · 0 assignees ·
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old niftyreg version Open
khanlab/neuroglia-core#2 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
khanlab/prepdwi#7 · 2 comments · 0 reactions · 0 assignees ·
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enhancement
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enhancement
khanlab/prepdwi#15 · 0 comments · 0 reactions · 1 assignee ·
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khanlab/hippunfold-templateflow#1 · 1 comment · 0 reactions · 0 assignees ·
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add a readthedocs Open
khanlab/hippunfold-templateflow#2 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/hippunfold-templateflow#3 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/hippunfold-templateflow#4 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/hippunfold-templateflow#5 · 0 comments · 0 reactions · 0 assignees ·
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R1map Open
khanlab/mp2rage_correction#1 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/funcmasker-flex#23 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/funcmasker-flex#26 · 1 comment · 0 reactions · 0 assignees ·
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bug
khanlab/autobids-globus#5 · 0 comments · 0 reactions · 1 assignee ·
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khanlab/autobids-portal#39 · 0 comments · 0 reactions · 0 assignees ·
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Expand Admin tab Open
khanlab/autobids-portal#40 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/autobids-portal#42 · 0 comments · 0 reactions · 0 assignees ·
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Fix/expand tests Open
khanlab/autobids-portal#47 · 1 comment · 0 reactions · 0 assignees ·
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khanlab/autobids-portal#107 · 1 comment · 0 reactions · 0 assignees ·
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khanlab/autobids-portal#183 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
khanlab/autobids-portal#209 · 0 comments · 0 reactions · 0 assignees ·
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Globus Limitations Openblocked bug
khanlab/autobids-portal#212 · 0 comments · 0 reactions · 0 assignees ·
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Custom heuristics Open
khanlab/autobids-portal#213 · 1 comment · 0 reactions · 1 assignee ·
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khanlab/hippunfold-plot#4 · 0 comments · 0 reactions · 0 assignees ·
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Plotly support Open
khanlab/hippunfold-plot#5 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/hippunfold-plot#6 · 0 comments · 0 reactions · 0 assignees ·
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contour overlay Openenhancement
khanlab/hippunfold-plot#7 · 1 comment · 0 reactions · 0 assignees ·
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synthseg slim Open
khanlab/synth_nnunet#1 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/diffparc-surf#4 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/diffparc-surf#5 · 0 comments · 0 reactions · 0 assignees ·
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Dicom import Open
khanlab/diffparc-surf#13 · 0 comments · 0 reactions · 0 assignees ·
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Test dataset Open
khanlab/diffparc-surf#14 · 0 comments · 0 reactions · 0 assignees ·
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README Open
khanlab/diffparc-surf#15 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/diffparc-surf#52 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/labelmerge#23 · 3 comments · 0 reactions · 0 assignees ·
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enhancement
khanlab/labelmerge#47 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/labelmerge#70 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/labelmerge#73 · 0 comments · 0 reactions · 0 assignees ·
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khanlab/tar2bids#20 · 0 comments · 0 reactions · 1 assignee ·
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khanlab/tar2bids#29 · 0 comments · 0 reactions · 0 assignees ·
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bug
khanlab/tar2bids#44 · 6 comments · 0 reactions · 0 assignees ·
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Singularity Openenhancement
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Tests Open
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BidsBatch Openenhancement
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Docstrings Opengood first issue
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bug
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enhancement
khanlab/kslurm#12 · 0 comments · 0 reactions · 0 assignees ·
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