chrisgorgo

chrisgorgo

def save_diffusion_vec(dcm_files, out_bvecs, out_bvals):
    bvals = []
    bvecs = []
    for dcm_file in dcm_files:
        dcm_dat = dicom.read_file(dcm_file)
        csa = nibabel.nicom.csareader.get_csa_header(dcm_dat)
        bval = nibabel.nicom.csareader.get_b_value(csa)
        bvec = nibabel.nicom.csareader.get_g_vector(csa)
        bvals.append(bval)
        bvecs.append(bvec)

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orange:nipype_test filo$ ./test.py
orange:nipype_test filo$ ls -al /tmp/was_run
-rw-r--r--  1 filo  wheel  0 Nov 19 12:21 /tmp/was_run
orange:nipype_test filo$ rm -rf /tmp/was_run
orange:nipype_test filo$ python simple_interface.py
gzip test.txt
orange:nipype_test filo$ ls -al /tmp/was_run
ls: /tmp/was_run: No such file or directory

chrisgorgo

chrisgorgo

import numpy as np
import dicom, nibabel.nicom.csareader

def save_diffusion_vec(dcm_files, out_bvecs, out_bvals):
    bvals = []
    bvecs = []
    for dcm_file in dcm_files:
        dcm_dat = dicom.read_file(dcm_file)
        csa = nibabel.nicom.csareader.get_csa_header(dcm_dat)
        bval = nibabel.nicom.csareader.get_b_value(csa)

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source_folder = "/Volumes/Samsung_T1/bids_examples/symlinked"
target_folder = "/Volumes/Samsung_T1/bids_examples/empty"

import shutil, os
from glob import glob
try:
    shutil.rmtree(target_folder)
except:
    pass

chrisgorgo

#pip install git+https://github.com/NeuroVault/pyneurovault
from pyneurovault import api
import numpy as np

all_collections = api.get_collections()
collections_with_dois = all_collections[np.logical_not(all_collections.DOI.isnull())]

images = api.get_images(collection_pks=list(collections_with_dois.collection_id))

# Remove images that are thresholded

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#!/usr/bin/python

import os, shutil, errno
import nipype
from nipype.interfaces import fsl, ants, c3
from nipype.caching import Memory
from nipype.interfaces.utility import IdentityInterface, Merge

#set up variables
datadir = "/scratch/users/macshine/data/nki/0102157"

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axis = 2

new_shape = list(x.shape)
del new_shape[axis]
a1, a2 = np.indices(new_shape)
inds = [a1, a2]
inds.insert(axis, x.argmax(axis=axis))
x[inds[0], inds[1], inds[2]]

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{% extends "base.html" %}
{% load crispy_forms_tags %}
{% load coffeescript %}
{% block head %}
<script src="{% static "scripts/clone-form.js"%}" type="text/javascript"></script>
	:javascript
		request_method = '{{request.method}}'
		{% inlinecoffeescript %}

			active_form = 0