satra

[alias]
        lg = "log --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr) %C(bold blue)[%an]%Creset' --abbrev-commit --date=relative"
        co = checkout
        st = "status -s"
        ci = commit
        br = branch
        bra = "branch -a"
        fo = "fetch origin"
        fu = "fetch upstream"

satra

In [2]: from enthought.traits.api import HasTraits, Int

In [3]: from cPickle import dumps, loads

In [9]: a = HasTraits()

In [10]: a.add_trait('foo', Int)

In [11]: a.foo = 1

satra

(ipxi)[satra@robinhill pyzmq (master)]$ python setup.py configure --zmq=/software/venvs/EPD/7.0/ipxi/
running configure
******************************************
Configure: Autodetecting ZMQ settings...
    Custom ZMQ dir:       /software/venvs/EPD/7.0/ipxi/
cc -I/software/venvs/EPD/7.0/ipxi/include -Izmq/utils -Izmq/core -Izmq/devices -c detect/vers.c -o detect/vers.o
cc -arch x86_64 -undefined dynamic_lookup detect/vers.o -L/software/venvs/EPD/7.0/ipxi/lib -lzmq -o detect/vers
    ZMQ version detected: 2.1.7
******************************************
(ipxi)[satra@robinhill pyzmq (master)]$ python setup.py install

satra

ANTS : http://picsl.upenn.edu/ANTS/ c3d : http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D

export PATH=/software/ANTS-dev:$PATH

c3d_affine_tool -ref [A] -src [B] bbreg.mat -fsl2ras -oitk fsl2antsAffine.txt

WarpImageMultiTransform 3 [B] [C] -R [D] [A_Warp].nii.gz [A_Affine].txt fsl2antsAffine.txt

satra

import os

import nipype.interfaces.utility as niu
import nipype.interfaces.io as nio
import nipype.interfaces.fsl as fsl
import nipype.pipeline.engine as pe

inputspec = pe.Node(niu.IdentityInterface(fields=['frac']),
                    name='inputsource')
inputspec.iterables = ('frac', [0.3, 0.5])

satra

In [2]: dcalc = Threedcalc()

In [3]: dcalc.inputs.infile_a = 'struct.nii'

In [4]: dcalc.inputs.expr = 'a'

In [5]: dcalc.cmdline
Out[5]: '3dcalc -a struct.nii -expr a -prefix /software/temp/struct_3dcalc.nii'

In [6]: dcalc.inputs.start_idx = 1

satra

In [1]:

cd /software/temp/nipype-tutorial/temp/
/software/temp/nipype-tutorial/temp
In [2]:

ls INBET
s1struct.nii  s3struct.nii
In [3]:

satra

from nipype.utils.logger import logging, logger, fmlogger, iflogger
logger.setLevel(logging.getLevelName('CRITICAL'))
fmlogger.setLevel(logging.getLevelName('CRITICAL'))
iflogger.setLevel(logging.getLevelName('CRITICAL'))

satra

>> disp('Eig');tic;data=rand(500,500);eig(data);toc;
disp('Svd');tic;data=rand(1000,1000);[u,s,v]=svd(data);s=svd(data);toc;
disp('Inv');tic;data=rand(1000,1000);result=inv(data);toc;
disp('Det');tic;data=rand(1000,1000);result=det(data);toc;
disp('Dot');tic;a=rand(1000,1000);b=inv(a);result=a*b-eye(1000);toc;
disp('Done');
Eig
Elapsed time is 0.840714 seconds.
Svd
Elapsed time is 1.931674 seconds.

satra

from enthought.mayavi import mlab
import streamlines
import numpy as np
from nibabel import load
from colorsys import rgb_to_hsv

# filename = "DeterministicTractography/QBALLRecon/hardiO10.trk"

trkfilename = "/software/data/STUT/DTI_TV/PWS04/dtk_35/dti_35.trk" #%hardiO10.trk_cross_streamline_id_20.trk"
bfilename =  "/software/data/STUT/DTI_TV/PWS04/dt_recon/lowb.nii"