Difference between revisions of "Analysis with Nipype"

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'''UNDER CONSTRUCTION'''
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'''UNDER CONSTRUCTION'''<br>
'''Nipype is a pipeline configuration tool that controls analysis flow and easily reconfigures for added functionality'''<br>
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'''Nipype is a pipeline configuration tool that controls analysis flow and easily reconfigures for added functionality.
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Nipye controls the flow of data and automatically determines dependencies to create filenames and folders'''<br>
   
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[[Image:Nipype meg.png]]
[[
 
   
 
Nipype configuration for Biowulf <br>
 
Nipype configuration for Biowulf <br>
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*Make install
 
*Make install
 
*Make usersite (will add a link so package is seen in conda)
 
*Make usersite (will add a link so package is seen in conda)
pull SAMsrcV5
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pull SAMsrcV5 <br>
pull megblocks
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pull megblocks <br>
install miniconda (or Anaconda)
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install miniconda (or Anaconda) <br>
 
*Add environment information to miniconda ##Need to provide environment.yml
 
*Add environment information to miniconda ##Need to provide environment.yml
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*Add pyctf, SAMsrc, and megblocks to the miniconda environment ## TODO < provide a way to do this. Add the paths to miniconda/env......pth file
*Add pyctf, SAMsrc,
 
   
   

Revision as of 11:06, 24 January 2020

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

  • 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