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b/notebooks/ni_viewer.ipynb |
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{ |
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"cells": [ |
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{ |
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"cell_type": "code", |
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"execution_count": null, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"import nibabel as nib\n", |
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"import os\n", |
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"from nilearn.image import crop_img\n", |
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"from nilearn.image import new_img_like, resample_to_img\n", |
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"import numpy as np" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": null, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"!ls ../brats/prediction/35" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": null, |
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"metadata": { |
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"scrolled": true |
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}, |
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"outputs": [], |
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"source": [ |
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"src_dir = '../brats/prediction/'\n", |
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"subject_id = '35'\n", |
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"vol = nib.load(os.path.join(src_dir, subject_id, 'data_volume.nii.gz'))" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": null, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"%matplotlib" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": null, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"vol.orthoview()" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": null, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"import sys\n", |
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"sys.path.append('..')" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": null, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"from fetal_new import augment" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": null, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"augment.distort_image()" |
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] |
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} |
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], |
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"metadata": { |
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"kernelspec": { |
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"display_name": "Python 3", |
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"language": "python", |
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"name": "python3" |
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}, |
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"language_info": { |
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"codemirror_mode": { |
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"name": "ipython", |
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"version": 3 |
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}, |
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"file_extension": ".py", |
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"mimetype": "text/x-python", |
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"name": "python", |
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"nbconvert_exporter": "python", |
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"pygments_lexer": "ipython3", |
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"version": "3.6.6" |
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} |
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}, |
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"nbformat": 4, |
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"nbformat_minor": 1 |
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} |