Analysis with Nipype

UNDER CONSTRUCTION Nipype is a pipeline configuration tool that controls analysis flow and easily reconfigures for added functionality

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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 - 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