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


Nipype configuration for Biowulf
pull pyctf

  • 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,

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 -
  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