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Oscar Esteban oesteban

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oesteban / createjson.py

Last active August 8, 2016 19:12

an API-created gist

	#!/opt/conda/bin/python
	"""
	Convert files to json objects uploadable to GitHub gists using:

	curl -v -H "Authorization: token <insert token here>" -X POST https://api.github.com/gists --data @<filename.json>

	"""

	import sys
	import json

oesteban / nose3.log

Created August 8, 2016 19:00

an API-created gist

This file has been truncated, but you can view the full file.

	nose.config: INFO: Ignoring files matching ['^\\.', '^_', '^setup\\.py$']
	nose.plugins.cover: INFO: Coverage report will include only packages: ['nipype']
	nose.selector: INFO: /root/src/nipype/nipype/interfaces/tests/use_resources is executable; skipped
	/root/src/nipype/nipype/workflows/dmri/mrtrix/group_connectivity.py:15: UserWarning: cmp not installed
	warnings.warn('cmp not installed')
	Doctest: nipype.algorithms.mesh ... ok
	Doctest: nipype.algorithms.metrics ... ok
	Doctest: nipype.algorithms.metrics.ErrorMap ... ok
	Doctest: nipype.algorithms.metrics.FuzzyOverlap ... ok
	Doctest: nipype.algorithms.metrics.Overlap ... ok

oesteban / autossh init.d

Created July 26, 2016 17:10 — forked from atr000/autossh init.d

launches and maintains uniquely named autossh tunnels alive

	#! /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
	#

oesteban / remove_output.py

Created June 6, 2016 18:51 — forked from damianavila/remove_output.py

Remove output from IPython notebook from the command line (dev version 1.0)

	"""
	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 / travis-neurodebian.sh

Last active February 13, 2016 20:00

	#!/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 / slice_contours.cpp

Last active August 29, 2015 14:10

A sliced 3D volume writer, with contours

	// --------------------------------------------------------------------------------------
	// 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 / myecc.sch

Created September 5, 2014 09:11

A FLIRT schedule for eddy correction

	# 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 / myhmc.sch

Last active August 29, 2015 14:06

A FLIRT schedule file for head-motion correction

	# 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 / SamplingUniformSphere.py

Created September 20, 2013 22:59


	#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 / SurfaceTransforms.py

Created September 10, 2013 19:40

Old code for transforming surfaces from freesurfer

	# 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]