satra

#DOES NOT WORK: GIFTI READ/WRITE is broken
import nibabel as nb
import nibabel.gifti as gifti

# load combined file
# created with: mris_convert --combinesurfs lh.pial rh.pial ./pial.gii
surf = gifti.read('pial.gii')

#load orig affine transform
ao = nb.load('orig.nii').get_affine()

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import os

from nipype import logging, config
config.set('logging', 'workflow_level', 'DEBUG')
logging.update_logging(config)

from nipype.pipeline.engine import Node, Workflow
from nipype.interfaces.utility import Function

def createtwofiles():

satra

from nipype.interfaces.fsl import BET
res = BET(in_file='struct.nii').run()
import nipype.external.prov as prov
import nipype.external.provgraph as pg
g = prov.json.load(open('provenance.json'), cls=prov.ProvBundle.JSONDecoder)
dot = pg.prov_to_dot(g)
dot.set_dpi(120)
dot.write_png('test.png')

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def isMoco(dcmfile):
    """Determine if a dicom file is a mocoseries
    """
    import subprocess
    cmd = ['mri_probedicom', '--i', dcmfile, '--t', '8', '103e']
    proc  = subprocess.Popen(cmd,
                             stdout=subprocess.PIPE,
                             stderr=subprocess.PIPE)
    stdout, stderr = proc.communicate()
    return stdout.strip().startswith('MoCoSeries')

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name of display: :0.0
display: :0  screen: 0
direct rendering: Yes
server glx vendor string: Chromium
server glx version string: 1.3 Chromium
server glx extensions:
    GLX_ARB_multisample, GLX_EXT_texture_from_pixmap, GLX_SGIX_fbconfig, 
    GLX_ARB_get_proc_address
client glx vendor string: Chromium
client glx version string: 1.3 Chromium

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bundle
  prefix foaf <http://xmlns.com/foaf/0.1/>
  prefix nipype <http://nipy.org/nipype/terms/0.6>
  prefix dcterms <http://purl.org/dc/terms/>
  
  activity(nipype:d21d596e2e0b11e2a1c714109fcf6ae7, 2012-11-14T03:31:39.567795, 2012-11-14T03:31:47.918502, [nipype:command="bet struct.nii /software/temp/nipype-tutorial/temp/provenance/struct_brain.nii.gz", prov:label="BET", prov:type='nipype:BET', nipype:working_directory="/software/temp/nipype-tutorial/temp/provenance", nipype:command_path="/usr/local/fsl/bin/bet", nipype:return_code=0, nipype:platform="Darwin-12.2.0-x86_64-i386-64bit", nipype:dependencies="/usr/local/fsl/bin/bet: is not an object file", nipype:duration="0.0" %% xsd:float, foaf:host="warpspeed.local"])
  collection(nipype:d21e243a2e0b11e2914a14109fcf6ae7, [prov:type='nipype:environment'])
  used(nipype:d21d596e2e0b11e2a1c714109fcf6ae7, nipype:d21e243a2e0b11e2914a14109fcf6ae7, -)
  entity(nipype:d21e2aeb2e0b11e2884f14109fcf6ae7, [prov:type='nipype:environment', nipype:ANTSPATH="/software/ANTSb

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[INFO] ------------------------------------------------------------------------
[INFO] Building PROV-N 0.0.2-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ prov-n ---
[INFO] Deleting /software/nipy-repo/ProvToolbox/prov-n/target
[INFO] 
[INFO] --- antlr3-maven-plugin:3.4:antlr (default) @ prov-n ---
[INFO] ANTLR: Processing source directory /software/nipy-repo/ProvToolbox/prov-n/src/main/antlr3
ANTLR Parser Generator  Version 3.4

satra

['FlowEncodingDirectionString',
 'PixelFile',
 'OriginalSeriesNumber',
 'RepetitionTimeEffective',
 'EchoLinePosition',
 'Comp_Algorithm',
 'ProtocolSliceNumber',
 'MoCoQMeasure',
 'NumberOfAverages',
 'VoxelNormalSag',

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rocessing regular_brain_ec_tmp0000

Final result: 
1.000000 0.000151 0.000000 -0.017864 
0.000000 1.000000 -0.000121 0.007878 
0.000000 0.000000 1.000000 -0.000000 
0.000000 0.000000 0.000000 1.000000 

processing regular_brain_ec_tmp0001

satra

# -*- coding: utf-8 -*-
# <nbformat>3</nbformat>

# <codecell>

import argparse
import os

from surfer import Brain
import scipy.io as sio