Software to Install

[gdevenyi]

NIFTI

• [x] afni
• [x] freesurfer
• [x] ANTs
• [x] mango
• [x] 3Dslicer
• [x] mricron
• [x] mricrogl
• [x] mrtrix3
• [x] itksnap
• [x] FSL
• [x] mi-brain
• [x] dcm2niix

python (all within conda env)

• [x] anaconda
• [x] bioconda
• [x] conda-forge
• [x] simpleitk
• [x] nibabel
• [x] nipype
• [x] nilearn
• [x] dipy
• [x] ANTsPy
• [x] jupyterlab
• [x] neurosynth
• [x] neuroquery

MINC

• [x] minc-toolkit-v2
• [x] pyminc
• [ ] minc2-simple
• [ ] generate_deformation_fields
• [x] CIVET
• [x] cobralab tools
• [ ] brain-view2

R

• [x] separate conda env
• [x] jupyter lab for R
• [x] rstudio
• [x] bioconductor
• [ ] ANTsR

MATLAB (packages)

• [ ] SPM
• [ ] SPM standalone
• [ ] Brainstorm
• [ ] Brainstorm standalone
• [ ] lead-dbs
• [ ] https://web.conn-toolbox.org/
• [ ] https://web.conn-toolbox.org/ standalone
• [ ] CAT12 http://www.neuro.uni-jena.de/cat/

Atlases

• [x] MNI models in MINC and NIFTI
• [x] cobralab atlases

[steelec]

Some ideas:

• Spm standalone,+packages? I can set those out if you want to go that far.
• eeg/meg based packages? There standards are in Matlab but there is a very nice one in Python as well. I think that brainstorm also has a standalone
• atlases linked in to a standard location?
• how do you feel about the whole containerization issue?
• missing the common resting state tool afni?

[gdevenyi]

@steelec

Your suggestions, while welcome, and a bit vague, do you have names or links for the stuff you're suggesting.

Also, can you move non-software package suggestions to #2 thanks.

[steelec]

And now you have now added most of them. Extras here: Python

• py-mne: https://mne.tools/stable/index.html
  • Required packages: https://raw.githubusercontent.com/mne-tools/mne-python/master/environment.yml
  • Source (most recent is in branch maint/0.19): https://github.com/mne-tools/mne-python.git

Matlab:

• eeglab https://sccn.ucsd.edu/wiki/How_to_download_EEGLAB

[gdevenyi]

https://brainstat.readthedocs.io/en/latest/generic/install.html