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| a | b/notebooks/ni_viewer.ipynb | ||
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| 1 | { |
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| 2 | "cells": [ |
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| 3 | { |
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| 4 | "cell_type": "code", |
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| 5 | "execution_count": null, |
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| 6 | "metadata": {}, |
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| 7 | "outputs": [], |
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| 8 | "source": [ |
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| 9 | "import nibabel as nib\n", |
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| 10 | "import os\n", |
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| 11 | "from nilearn.image import crop_img\n", |
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| 12 | "from nilearn.image import new_img_like, resample_to_img\n", |
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| 13 | "import numpy as np" |
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| 14 | ] |
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| 15 | }, |
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| 16 | { |
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| 17 | "cell_type": "code", |
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| 18 | "execution_count": null, |
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| 19 | "metadata": {}, |
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| 20 | "outputs": [], |
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| 21 | "source": [ |
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| 22 | "!ls ../brats/prediction/35" |
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| 23 | ] |
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| 24 | }, |
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| 25 | { |
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| 26 | "cell_type": "code", |
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| 27 | "execution_count": null, |
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| 28 | "metadata": { |
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| 29 | "scrolled": true |
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| 30 | }, |
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| 31 | "outputs": [], |
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| 32 | "source": [ |
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| 33 | "src_dir = '../brats/prediction/'\n", |
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| 34 | "subject_id = '35'\n", |
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| 35 | "vol = nib.load(os.path.join(src_dir, subject_id, 'data_volume.nii.gz'))" |
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| 36 | ] |
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| 37 | }, |
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| 38 | { |
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| 39 | "cell_type": "code", |
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| 40 | "execution_count": null, |
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| 41 | "metadata": {}, |
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| 42 | "outputs": [], |
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| 43 | "source": [ |
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| 44 | "%matplotlib" |
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| 45 | ] |
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| 46 | }, |
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| 47 | { |
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| 48 | "cell_type": "code", |
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| 49 | "execution_count": null, |
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| 50 | "metadata": {}, |
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| 51 | "outputs": [], |
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| 52 | "source": [ |
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| 53 | "vol.orthoview()" |
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| 54 | ] |
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| 55 | }, |
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| 56 | { |
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| 57 | "cell_type": "code", |
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| 58 | "execution_count": null, |
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| 59 | "metadata": {}, |
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| 60 | "outputs": [], |
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| 61 | "source": [ |
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| 62 | "import sys\n", |
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| 63 | "sys.path.append('..')" |
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| 64 | ] |
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| 65 | }, |
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| 66 | { |
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| 67 | "cell_type": "code", |
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| 68 | "execution_count": null, |
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| 69 | "metadata": {}, |
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| 70 | "outputs": [], |
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| 71 | "source": [ |
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| 72 | "from fetal_new import augment" |
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| 73 | ] |
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| 74 | }, |
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| 75 | { |
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| 76 | "cell_type": "code", |
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| 77 | "execution_count": null, |
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| 78 | "metadata": {}, |
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| 79 | "outputs": [], |
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| 80 | "source": [ |
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| 81 | "augment.distort_image()" |
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| 82 | ] |
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| 83 | } |
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| 84 | ], |
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| 85 | "metadata": { |
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| 86 | "kernelspec": { |
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| 87 | "display_name": "Python 3", |
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| 88 | "language": "python", |
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| 89 | "name": "python3" |
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| 90 | }, |
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| 91 | "language_info": { |
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| 92 | "codemirror_mode": { |
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| 93 | "name": "ipython", |
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| 94 | "version": 3 |
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| 95 | }, |
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| 96 | "file_extension": ".py", |
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| 97 | "mimetype": "text/x-python", |
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| 98 | "name": "python", |
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| 99 | "nbconvert_exporter": "python", |
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| 100 | "pygments_lexer": "ipython3", |
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| 101 | "version": "3.6.6" |
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| 102 | } |
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| 103 | }, |
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| 104 | "nbformat": 4, |
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| 105 | "nbformat_minor": 1 |
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| 106 | } |