Analysis with Nipype

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UNDER CONSTRUCTION
Nipype is a pipeline configuration tool that controls analysis flow and easily reconfigures for added functionality. Nipye controls the flow of data and automatically determines dependencies to create filenames and folders

Nipype meg.png

Nipype configuration for Biowulf

pull pyctf

 module load fftw.....  # first do a module spide fftw and find one to use
 Navigate to top folder (with Makefile)
 Make clean
 Make
 Make install
 Make usersite  (will add a link so package is seen in conda)

pull SAMsrcV5
pull megblocks
install miniconda (or Anaconda)

  • Add environment information to miniconda ##Need to provide environment.yml
  • Add pyctf, SAMsrc, and megblocks to the miniconda environment ## TODO < provide a way to do this. Add the paths to miniconda/env......pth file


Nipype has strict requirements on inputs and outputs

  1. InputSpec
  2. OutputSpec



Preconfigured pipeline templates:

  1. Epilepsy
    1. Sam_epi
  2. Task
    1. Parsemarks, addmarks, samcov, sam3d, ... stats?
  3. Resting State


SAM input base class used for all of the SAM functions


Configuration on Biowulf:

  1. Set up conda: instructions on NIH HPC - https://hpc.nih.gov/apps/python.html
  2. Activate the conda environment and install nipype
 #If you do not know your environment name type: conda env list
 conda activate $ENVIRONMENT_NAME   
 conda install -c nipype conda-forge