satra

satra

img = nib.load(imgfile)
bvecs = np.genfromtxt(bvecs)
    
def get_trackvis_mat(aff):
    """based on input from ruopeng @ tracvkis
    """
    for i in range(10):
        #aff = aff.dot(np.linalg.inv(np.eye(3) + 3*aff.T.dot(aff)).dot(3*np.eye(3) + aff.T.dot(aff)))
        aff = 0.5 * (aff + np.linalg.inv(aff.T))
    return np.dot(aff, np.array([[1,0,0],[0,-1,0],[0,0,1]]))

satra

#!/usr/bin/env python
#
# Demo to return a file with a uri delivered by a virtuoso server

import md5
import json
import os
from urlparse import urlparse

import cherrypy

satra

#!/usr/bin/env python

# Convert dicom 2 nrrd
def dicom2nrrd(dicomdir, out_prefix):
    import os
    from nipype.interfaces.base import CommandLine
    cmd = CommandLine('DWIConvert --inputDicomDirectory %s --outputVolume %s.nrrd' % (dicomdir, out_prefix))
    cmd.run()
    return os.path.abspath('%s.nrrd' % out_prefix)

satra

import os

from hashlib import md5
import rdflib
from rdflib.namespace import Namespace, NamespaceManager, RDF, FOAF, XSD
from rdflib import URIRef, BNode, Literal
from uuid import uuid1
from socket import getfqdn

db_location = os.path.join(os.getcwd(), 'database.ttl')

satra

# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>

# <codecell>

from glob import glob
import os

import numpy as np

satra

satra

Step 0: recon-all -subjid H0351.1015 -all -i /data/allen/H0351.1015/T1.nii.gz -openmp 8 -notalairach

Step 1: recon-all -subjid H0351.1015 -T2 /data/allen/H0351.1015/T2.nii.gz -openmp 8

Step 2: recon-all -subjid H0351.1015 -T2pial -openmp 8

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

satra

import argparse
import os

from nipype.pipeline.engine import Workflow, Node, MapNode
from nipype.interfaces.utility import IdentityInterface
from nipype.interfaces.fsl.utils import ImageMaths
from nipype.interfaces.fsl.utils import Split
from nipype.interfaces.fsl.dti import XFibres
from nipype.interfaces.fsl.utils import Merge
from nipype.interfaces.fsl.dti import MakeDyadicVectors

satra

from surfer import Brain
lh = Brain('fs404', 'lh', 'pial')
rh = Brain('fs404', 'rh', 'pial', figure=lh._f)
lh.add_annotation('aparc', borders=False, alpha=0)
rh.add_annotation('aparc', borders=False, alpha=0.5)
"""
lh._geo_surf.actor.property.opacity = 0.3
rh._geo_surf.actor.property.opacity = 0.3
lh._geo_surf.contour.contours = [0.5]
lh._geo_surf.actor.mapper.progress = 1.0