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Initially included packages #3

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16 of 51 tasks
joschaschmiedt opened this issue Feb 7, 2023 · 8 comments
Closed
16 of 51 tasks

Initially included packages #3

joschaschmiedt opened this issue Feb 7, 2023 · 8 comments

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@joschaschmiedt
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joschaschmiedt commented Feb 7, 2023 •
edited

Here we collect the neuroscience-related packages that we initially attempt to support:

Electrophysiology

Neuroimaging

  • nipype
  • dipy
  • mindboogle
  • nibabel
  • napari-nibabel
  • scitran SDM
  • nipy
  • nibabel
  • Scitran SDM
  • nipy
  • nitime
  • popeye
  • nilearn
  • pymvpa
  • mne
  • mnelab
  • mne-realtime
  • mne-rsa
  • mne-nirs
  • mne-icalabel
  • mne-connectivity
  • mne-features
  • mne-bids
  • mne-bids-pipeline
  • mne-ari
  • niwidgets
  • pybids
  • nistats
  • imageio
  • pydicom
  • deid
  • intensity-normalization

Implicit, useful dependencies

  • numpy
  • scipy
  • matplotlib
  • scikit-learn
  • jupyter
  • hdf5

Some further candidates
@joschaschmiedt
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joschaschmiedt commented Feb 22, 2023 •
edited

Interesting package lists

@pantaray
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pantaray commented Feb 23, 2023 •
edited by joschaschmiedt

Here some specifically (f)MRI/MEG-related packages (the first half is taken from nipy.org):

  • nipype
  • dipy
  • mindboogle
  • nibabel
  • napari-nibabel
  • scitran SDM
  • nipy
  • nibabel
  • Scitran SDM
  • nipy
  • nitime
  • popeye
  • nilearn
  • pymvpa
  • mne
  • mnelab
  • mne-realtime
  • mne-rsa
  • mne-nirs
  • mne-icalabel
  • mne-connectivity
  • mne-features
  • mne-bids
  • mne-bids-pipeline
  • mne-ari
  • niwidgets
  • pybids
  • nistats
  • imageio
  • pydicom
  • deid
  • intensity-normalization

Most ML-MRI-analysis-packages additionally rely on PyTorch or Tensorflow. Most notably:

  • fastMRI
  • Deep-MRI-Reconstruction

Additionally, many pipeline-packages mix and match routines of the "standard" fMRI processing suties AFNI, FSL, ANTs and Freesurfer. Most notably:

  • mriqc
  • fMRIPrep
  • sMRIPrep

Unless you have any objections, I think we might want to initially focus on the non-ML Python-only packages in the first list above.

@joschaschmiedt
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Unless you have any objections, I think we might want to initially focus on the non-ML Python-only packages in the first list above.

Agreed.

@joschaschmiedt
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@pantaray, would you mind to try out how difficult adding some of the neuroimaging packages is?

@pantaray
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pantaray commented Mar 1, 2023

Not at all! If it's okay, I'd focus again on macOS and Linux for the time being.

@joschaschmiedt
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Suggestions from @davrot

  • tqdm
  • argh
  • pywavelets
  • scikit-learn
  • ( ipympl )
  • ( opencv-python )
  • ( scikit-image )

This was referenced Mar 3, 2023
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@joschaschmiedt
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joschaschmiedt commented Mar 3, 2023 •
edited

I'm closing this issue as we have follow-up issues #20, #27 #21 , #22 , #23 , #24

@davrot
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davrot commented Mar 3, 2023

Status unclear:
mindboogle (needs docker container?)
pymvpa
intensity-normalization

Dead project:
scitran SDM
https://github.com/scitran/sdm

broken ?
niwidgets

version problem:
pigar

neuro-conda-latest.yml.txt
log_03032023b.txt

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@joschaschmiedt @pantaray @davrot