oesteban

# -*- coding: utf-8 -*-
# Author: Douglas Creager <[email protected]>
# This file is placed into the public domain.

# Calculates the current version number.  If possible, this is the
# output of “git describe”, modified to conform to the versioning
# scheme that setuptools uses.  If “git describe” returns an error
# (most likely because we're in an unpacked copy of a release tarball,
# rather than in a git working copy), then we fall back on reading the
# contents of the RELEASE-VERSION file.

oesteban

from mayavi import mlab
from tvtk.api import tvtk
import numpy as np


surfname = os.path.join( model_path, 'fixed.csf.vtk' )
reader =tvtk.PolyDataReader( file_name=surfname )
mesh = reader.get_output()
reader.update()

oesteban

# http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms
tkr1_tfm = fsbt.mri_info( op.join( tpms_dir, 'wm_volume_fraction.nii.gz' ), 'vox2ras-tkr' )
r2v_tfm = fsbt.mri_info( op.join( tpms_dir, 'wm_volume_fraction.nii.gz' ), 'ras2vox' )

tkr2_tfm = fsbt.mri_info( op.join( tpms_dir, 'wm_volume_fraction.nii.gz' ), 'ras2vox-tkr' )
v2r_tfm = fsbt.mri_info( op.join( tpms_dir, 'wm_volume_fraction.nii.gz' ), 'vox2ras' )

tfm = np.dot( tkr2_tfm, v2r_tfm )
M = tfm[0:3,0:3]
O = tfm[0:3,3]

oesteban

#http://stackoverflow.com/questions/15880367/python-uniform-distribution-of-points-on-4-dimensional-sphere
dim = 3

norm = np.random.normal
normal_deviates = norm(size=(dim, N))

radius = np.sqrt((normal_deviates**2).sum(axis=0))
points = normal_deviates/radius
points = points.reshape(-1,3)

oesteban

# 4mm scale
setscale 4
setoption smoothing 6
clear U
clear UA 
clear UB
clear US
clear UP
# try the identity transform as a starting point at this resolution
clear UQ

oesteban

# 4mm scale
setscale 4
setoption smoothing 6
setoption paramsubset 1  0 0 0 0 0 0 1 1 1 1 1 1
clear U
clear UA 
clear UB
clear US
clear UP
# try the identity transform as a starting point at this resolution

oesteban

// --------------------------------------------------------------------------------------
// File:          slice_contours.cxx
// Date:          Nov 18, 2014
// Author:        [email protected] (Oscar Esteban)
// Version:       1.0 beta
// License:       GPLv3 - 29 June 2007
// Short Summary:
// --------------------------------------------------------------------------------------
//
// Copyright (c) 2014, [email protected] (Oscar Esteban)

oesteban

#!/bin/bash

# A universal helper to enable NeuroDebian repository for a travis
# environment.
#
# Its purpose to remove all repetative actions from various .travis.yml spread
# across projects and gain control in the future to point  to an alternative,
# more appropriate for travis deployments, mirror.

# for the protocol

oesteban

"""
Usage: python remove_output.py notebook.ipynb [ > without_output.ipynb ]
Modified from remove_output by Minrk

"""
import sys
import io
import os
from IPython.nbformat.current import read, write

oesteban

#! /bin/sh
#
# Author:	Andreas Olsson <[email protected]>
# Version:	@(#)autossh_tunnel.foo  0.1  27-Aug-2008  [email protected]
#
# For each tunnel; make a uniquely named copy of this template.


## SETTINGS
#