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Neuroinformatics Pipelines
A page to store links to documentation for common bits of software, and take notes on steps that overlap. I think that, by and large, the majority of neuroscience problems fall into three categories: image manipulation, quantifying behavioral observations, manipulating physiological observations, and stimulus presentation.
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These utilities ultimately should amount to specialized versions of Photoshop/the GIMP that operate in 3D space rather than 2D. Some of them include some statistical processing tools as well. Essentially these then become hybridized versions of Photoshop and R/Stata/SPSS/SAS.
- RELION
- SPM12
- AFNI
- ANTS
- BROCCOLI
- Brainstorm
- BrainVoyager
- ITK
- BEaST (also here)
- Imaging Software Installed by the NIH
- MNI Tools
- Neurolucida
As per earlier statements, compare these manuals to:
- Ilastik
- OpenCV
- scikitiimage
- vips
- Tomopy
- netpbm (AFNI dependency)
- ImageMagick
- Bioread (for BIOPAC)
Stimulus presentation packages, by their very nature, also quantify behavioral data into reaction times and specific responses.