satra

import os

import numpy as np

from nipype.interfaces.spm import *
import nipype.interfaces.matlab as mlab      # how to run matlab

mlab.MatlabCommand.set_default_matlab_cmd("matlab -nodesktop -nosplash")
mlab.MatlabCommand.set_default_paths('/software/spm8')

satra

#! /usr/bin/env python

import argparse

from nipype.utils.filemanip import loadcrash

def display_crash_files(crashfile, rerun):
    "display crash file content and rerun if required"
    crash_data = loadcrash(crashfile)
    node = crash_data['node']

satra

import os

from nipype.interfaces.base import (CommandLine, CommandLineInputSpec,
                                    TraitedSpec, File,
                                    InputMultiPath, traits)
from nipype.utils.misc import isdefined
from nipype.utils.filemanip import fname_presuffix

class ITKNaryMaximumImageFilterInputSpec(CommandLineInputSpec):
    tcl_script = File(exists=True, argstr = '-b %s', position = 1,

satra

l2BGflow = pe.Workflow(name='l2BGflow')
# setup a between group 2-sample t-test node
twosamplettestdes = pe.Node(interface=spm.TwoSampleTTestDesign(), name="twosampttestdes")
twosamplettestdes.inputs.explicit_mask_file = os.path.abspath('/software/spm8/apriori/brainmask.nii')
l2BGestimate = pe.Node(interface=spm.EstimateModel(), name="twosampleestimate")
l2BGestimate.inputs.estimation_method = {'Classical' : 1}
l2BGconestimate = pe.Node(interface = spm.EstimateContrast(), name="twosampleconestimate")
con_1 = ('Controls','T', ['Group_{1}'],[1])
con_2 = ('Patients','T', ['Group_{2}'],[1])
con_3 = ('Controls>Patients','T',['Group_{1}','Group_{2}'],[1,-1])

satra

"""
Preprocess the Haxby data with SPM+FSL: normalize to MNI
"""
import os
import urllib
import tarfile
import gzip
import glob
import shutil

satra

from EPD install:

As the last step, you should edit your .bashrc or prepend
the EPD install path:

    /software/python/EPD/7.0/bin

Thank you for installing EPD!

$ export PATH=/software/python/EPD/7.0/bin:$PATH

satra

Please note that this gist applies to EPD version 7.0 and 7.1. EPD 7.1 includes ETS 
but not completely on OSX x64. Furthermore a patch has been submitted for inclusion 
in virtualenv that should resolve the virtualenv issue.

The notes below were compiled for 7.0 and will need to be replaced with corresponding
7.1 paths.

https://github.com/satra/virtualenv/tree/fix/EPDpatch

satra

"""Example script that executes via SGE qsub
"""
import nipype.pipeline.engine as pe
import nipype.interfaces.matlab as mlab
import nipype.interfaces.spm as spm
import os

mlab.MatlabCommand.set_default_matlab_cmd("matlab -nodesktop -nosplash")
mlab.MatlabCommand.set_default_paths('/software/spm8')

satra

In [19]: class A(HasTraits):
    foo = Int
    def __init__(self, **kwargs):
        super(A, self).__init__(**kwargs)
        self.on_trait_change(self.raiseerror, 'foo')
    def raiseerror(self, obj, name, old, new):
        raise Exception('testing exception')
   ....:     
   ....:     

satra

class Stream(object):
    """Function to capture stdout and stderr streams with timestamps

    http://stackoverflow.com/questions/4984549/merge-and-sync-stdout-and-stderr/5188359#5188359
    """

    def __init__(self, name, impl):
        self._name = name
        self._impl = impl
        self._buf = ''