Difference between revisions of "Analysis with Nipype"

From MEG Core
Jump to navigation Jump to search
m (Save before image upload)
Line 1: Line 1:
  +
'''UNDER CONSTRUCTION'''
 
'''Nipype is a pipeline configuration tool that controls analysis flow and easily reconfigures for added functionality'''<br>
 
'''Nipype is a pipeline configuration tool that controls analysis flow and easily reconfigures for added functionality'''<br>
  +
  +
[[
  +
  +
Nipype configuration for Biowulf <br>
  +
pull pyctf <br>
  +
*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 <br>
 
Nipype has strict requirements on inputs and outputs <br>

Revision as of 10:56, 24 January 2020

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 - 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