somada141

Imports:

import vtk
from vtk.util import numpy_support
import numpy

Create a vtkDICOMImageReader object, set its directory to the one containing all DICOM files, and Update to read in all data:

rvl

Pushing to Multiple Git Repos

If a project has to have multiple git repos (e.g. Bitbucket and Github) then it's better that they remain in sync.

Usually this would involve pushing each branch to each repo in turn, but actually Git allows pushing to multiple repos in one go.

If in doubt about what git is doing when you run these commands, just

albertomontesg

ahmedhosny

import nrrd # pip install pynrrd
import nibabel as nib # pip install nibabel
import numpy as np

# load nrrd 
_nrrd = nrrd.read('/path/to/nrrd.nrrd')
data = _nrrd[0]
header = _nrrd[1]
print data.shape, header

gilrosenthal

!pip install fastai
!apt-get -qq install -y libsm6 libxext6 && pip install -q -U opencv-python
import cv2
from os import path
from wheel.pep425tags import get_abbr_impl, get_impl_ver, get_abi_tag
platform = '{}{}-{}'.format(get_abbr_impl(), get_impl_ver(), get_abi_tag())

accelerator = 'cu80' if path.exists('/opt/bin/nvidia-smi') else 'cpu'

!pip install -q http://download.pytorch.org/whl/{accelerator}/torch-0.3.0.post4-{platform}-linux_x86_64.whl torchvision

jcreinhold

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
nii_to_tif

command line executable to convert 3d nifti images to 
individual tiff images along a user-specified axis

call as: python nii_to_tif.py /path/to/nifti /path/to/tif
(append optional arguments to the call as desired)

yashkumaratri

#CODE

#Generate root password
import random, string
password = ''.join(random.choice(string.ascii_letters + string.digits) for i in range(20))

#Download ngrok
! wget -q -c -nc https://bin.equinox.io/c/4VmDzA7iaHb/ngrok-stable-linux-amd64.zip
! unzip -qq -n ngrok-stable-linux-amd64.zip
#Setup sshd

jcreinhold

jcreinhold

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
tif_to_nii

command line executable to convert a directory of tif images
(from one image) to a nifti image stacked along a user-specified axis

call as: python tif_to_nii.py /path/to/tif/ /path/to/nifti
(append optional arguments to the call as desired)