Buckets:
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| <link rel="modulepreload" href="/docs/datasets/pr_8021/en/_app/immutable/chunks/CodeBlock.5919a092.js"><!-- HEAD_svelte-u9bgzb_START --><meta name="hf:doc:metadata" content="{"title":"Create a NIfTI dataset","local":"create-a-nifti-dataset","sections":[{"title":"Local files","local":"local-files","sections":[],"depth":2},{"title":"Folder conventions and metadata","local":"folder-conventions-and-metadata","sections":[],"depth":2},{"title":"Converting to PyTorch tensors","local":"converting-to-pytorch-tensors","sections":[],"depth":2},{"title":"Usage of NifTI1Image","local":"usage-of-nifti1image","sections":[],"depth":2},{"title":"For further reading we refer to the nibabel documentation and especially this nibabel tutorial","local":"for-further-reading-we-refer-to-the-nibabel-documentation-and-especially-this-nibabel-tutorial","sections":[],"depth":2}],"depth":1}"><!-- HEAD_svelte-u9bgzb_END --> <p></p> <div class="items-center shrink-0 min-w-[100px] max-sm:min-w-[50px] justify-end ml-auto flex" style="float: right; margin-left: 10px; display: inline-flex; position: relative; z-index: 10;"><div class="inline-flex rounded-md max-sm:rounded-sm"><button class="inline-flex items-center gap-1 h-7 max-sm:h-7 px-2 max-sm:px-1.5 text-sm font-medium text-gray-800 border border-r-0 rounded-l-md max-sm:rounded-l-sm border-gray-200 bg-white hover:shadow-inner dark:border-gray-850 dark:bg-gray-950 dark:text-gray-200 dark:hover:bg-gray-800" aria-live="polite"><span class="inline-flex items-center justify-center rounded-md p-0.5 max-sm:p-0 hover:text-gray-800 dark:hover:text-gray-200"><svg class="sm:size-3.5 size-3" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M28,10V28H10V10H28m0-2H10a2,2,0,0,0-2,2V28a2,2,0,0,0,2,2H28a2,2,0,0,0,2-2V10a2,2,0,0,0-2-2Z" transform="translate(0)"></path><path d="M4,18H2V4A2,2,0,0,1,4,2H18V4H4Z" transform="translate(0)"></path><rect fill="none" width="32" height="32"></rect></svg></span> <span>Copy page</span></button> <button class="inline-flex items-center justify-center w-6 max-sm:w-5 h-7 max-sm:h-7 disabled:pointer-events-none text-sm text-gray-500 hover:text-gray-700 dark:hover:text-white rounded-r-md max-sm:rounded-r-sm border border-l transition border-gray-200 bg-white hover:shadow-inner dark:border-gray-850 dark:bg-gray-950 dark:text-gray-200 dark:hover:bg-gray-800" aria-haspopup="menu" aria-expanded="false" aria-label="Open copy menu"><svg class="transition-transform text-gray-400 overflow-visible sm:size-3.5 size-3 rotate-0" width="1em" height="1em" viewBox="0 0 12 7" fill="none" xmlns="http://www.w3.org/2000/svg"><path d="M1 1L6 6L11 1" stroke="currentColor"></path></svg></button></div> </div> <h1 class="relative group"><a id="create-a-nifti-dataset" class="header-link block pr-1.5 text-lg no-hover:hidden with-hover:absolute with-hover:p-1.5 with-hover:opacity-0 with-hover:group-hover:opacity-100 with-hover:right-full" href="#create-a-nifti-dataset"><span><svg class="" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" aria-hidden="true" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 256 256"><path d="M167.594 88.393a8.001 8.001 0 0 1 0 11.314l-67.882 67.882a8 8 0 1 1-11.314-11.315l67.882-67.881a8.003 8.003 0 0 1 11.314 0zm-28.287 84.86l-28.284 28.284a40 40 0 0 1-56.567-56.567l28.284-28.284a8 8 0 0 0-11.315-11.315l-28.284 28.284a56 56 0 0 0 79.196 79.197l28.285-28.285a8 8 0 1 0-11.315-11.314zM212.852 43.14a56.002 56.002 0 0 0-79.196 0l-28.284 28.284a8 8 0 1 0 11.314 11.314l28.284-28.284a40 40 0 0 1 56.568 56.567l-28.285 28.285a8 8 0 0 0 11.315 11.314l28.284-28.284a56.065 56.065 0 0 0 0-79.196z" fill="currentColor"></path></svg></span></a> <span>Create a NIfTI dataset</span></h1> <p data-svelte-h="svelte-112h77q">This page shows how to create and share a dataset of medical images in NIfTI format (.nii / .nii.gz) using the <code>datasets</code> library.</p> <p data-svelte-h="svelte-12uzys7">You can share a dataset with your team or with anyone in the community by creating a dataset repository on the Hugging Face Hub:</p> <div class="code-block relative "><div class="absolute top-2.5 right-4"><button class="inline-flex items-center relative text-sm focus:text-green-500 cursor-pointer focus:outline-none transition duration-200 ease-in-out opacity-0 mx-0.5 text-gray-600 " title="code excerpt" type="button"><svg class="" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M28,10V28H10V10H28m0-2H10a2,2,0,0,0-2,2V28a2,2,0,0,0,2,2H28a2,2,0,0,0,2-2V10a2,2,0,0,0-2-2Z" transform="translate(0)"></path><path d="M4,18H2V4A2,2,0,0,1,4,2H18V4H4Z" transform="translate(0)"></path><rect fill="none" width="32" height="32"></rect></svg> <div class="absolute pointer-events-none transition-opacity bg-black text-white py-1 px-2 leading-tight rounded font-normal shadow left-1/2 top-full transform -translate-x-1/2 translate-y-2 opacity-0"><div class="absolute bottom-full left-1/2 transform -translate-x-1/2 w-0 h-0 border-black border-4 border-t-0" style="border-left-color: transparent; border-right-color: transparent; "></div> Copied</div></button></div> <pre class=""><!-- HTML_TAG_START --><span class="hljs-keyword">from</span> datasets <span class="hljs-keyword">import</span> load_dataset | |
| dataset = load_dataset(<span class="hljs-string">"<username>/my_nifti_dataset"</span>)<!-- HTML_TAG_END --></pre></div> <p data-svelte-h="svelte-tz8sxl">There are two common ways to create a NIfTI dataset:</p> <ul data-svelte-h="svelte-o3y4kh"><li>Create a dataset from local NIfTI files in Python and upload it with <code>Dataset.push_to_hub</code>.</li> <li>Use a folder-based convention (one file per example) and a small helper to convert it into a <code>Dataset</code>.</li></ul> <blockquote class="tip" data-svelte-h="svelte-sy3xkv"><p>You can control access to your dataset by requiring users to share their contact information first. Check out the <a href="https://huggingface.co/docs/hub/datasets-gated" rel="nofollow">Gated datasets</a> guide for more information.</p></blockquote> <h2 class="relative group"><a id="local-files" class="header-link block pr-1.5 text-lg no-hover:hidden with-hover:absolute with-hover:p-1.5 with-hover:opacity-0 with-hover:group-hover:opacity-100 with-hover:right-full" href="#local-files"><span><svg class="" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" aria-hidden="true" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 256 256"><path d="M167.594 88.393a8.001 8.001 0 0 1 0 11.314l-67.882 67.882a8 8 0 1 1-11.314-11.315l67.882-67.881a8.003 8.003 0 0 1 11.314 0zm-28.287 84.86l-28.284 28.284a40 40 0 0 1-56.567-56.567l28.284-28.284a8 8 0 0 0-11.315-11.315l-28.284 28.284a56 56 0 0 0 79.196 79.197l28.285-28.285a8 8 0 1 0-11.315-11.314zM212.852 43.14a56.002 56.002 0 0 0-79.196 0l-28.284 28.284a8 8 0 1 0 11.314 11.314l28.284-28.284a40 40 0 0 1 56.568 56.567l-28.285 28.285a8 8 0 0 0 11.315 11.314l28.284-28.284a56.065 56.065 0 0 0 0-79.196z" fill="currentColor"></path></svg></span></a> <span>Local files</span></h2> <p data-svelte-h="svelte-1q5vbiq">If you already have a list of file paths to NIfTI files, the easiest workflow is to create a <code>Dataset</code> from that list and cast the column to the <code>Nifti</code> feature.</p> <div class="code-block relative "><div class="absolute top-2.5 right-4"><button class="inline-flex items-center relative text-sm focus:text-green-500 cursor-pointer focus:outline-none transition duration-200 ease-in-out opacity-0 mx-0.5 text-gray-600 " title="code excerpt" type="button"><svg class="" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M28,10V28H10V10H28m0-2H10a2,2,0,0,0-2,2V28a2,2,0,0,0,2,2H28a2,2,0,0,0,2-2V10a2,2,0,0,0-2-2Z" transform="translate(0)"></path><path d="M4,18H2V4A2,2,0,0,1,4,2H18V4H4Z" transform="translate(0)"></path><rect fill="none" width="32" height="32"></rect></svg> <div class="absolute pointer-events-none transition-opacity bg-black text-white py-1 px-2 leading-tight rounded font-normal shadow left-1/2 top-full transform -translate-x-1/2 translate-y-2 opacity-0"><div class="absolute bottom-full left-1/2 transform -translate-x-1/2 w-0 h-0 border-black border-4 border-t-0" style="border-left-color: transparent; border-right-color: transparent; "></div> Copied</div></button></div> <pre class=""><!-- HTML_TAG_START --><span class="hljs-keyword">from</span> datasets <span class="hljs-keyword">import</span> Dataset | |
| <span class="hljs-keyword">from</span> datasets <span class="hljs-keyword">import</span> Nifti | |
| <span class="hljs-comment"># simple example: create a dataset from file paths</span> | |
| files = [<span class="hljs-string">"/path/to/scan_001.nii.gz"</span>, <span class="hljs-string">"/path/to/scan_002.nii.gz"</span>] | |
| ds = Dataset.from_dict({<span class="hljs-string">"nifti"</span>: files}).cast_column(<span class="hljs-string">"nifti"</span>, Nifti()) | |
| <span class="hljs-comment"># access a decoded nibabel image (if decode=True)</span> | |
| <span class="hljs-comment"># ds[0]["nifti"] will be a nibabel.Nifti1Image object when decode=True</span> | |
| <span class="hljs-comment"># or a dict {'bytes': None, 'path': '...'} when decode=False</span><!-- HTML_TAG_END --></pre></div> <p data-svelte-h="svelte-1czj1dy">The <code>Nifti</code> feature supports a <code>decode</code> parameter. When <code>decode=True</code> (the default), it loads the NIfTI file into a <code>nibabel.nifti1.Nifti1Image</code> object. You can access the image data as a numpy array with <code>img.get_fdata()</code>. When <code>decode=False</code>, it returns a dict with the file path and bytes.</p> <div class="code-block relative "><div class="absolute top-2.5 right-4"><button class="inline-flex items-center relative text-sm focus:text-green-500 cursor-pointer focus:outline-none transition duration-200 ease-in-out opacity-0 mx-0.5 text-gray-600 " title="code excerpt" type="button"><svg class="" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M28,10V28H10V10H28m0-2H10a2,2,0,0,0-2,2V28a2,2,0,0,0,2,2H28a2,2,0,0,0,2-2V10a2,2,0,0,0-2-2Z" transform="translate(0)"></path><path d="M4,18H2V4A2,2,0,0,1,4,2H18V4H4Z" transform="translate(0)"></path><rect fill="none" width="32" height="32"></rect></svg> <div class="absolute pointer-events-none transition-opacity bg-black text-white py-1 px-2 leading-tight rounded font-normal shadow left-1/2 top-full transform -translate-x-1/2 translate-y-2 opacity-0"><div class="absolute bottom-full left-1/2 transform -translate-x-1/2 w-0 h-0 border-black border-4 border-t-0" style="border-left-color: transparent; border-right-color: transparent; "></div> Copied</div></button></div> <pre class=""><!-- HTML_TAG_START --><span class="hljs-keyword">from</span> datasets <span class="hljs-keyword">import</span> Dataset, Nifti | |
| ds = Dataset.from_dict({<span class="hljs-string">"nifti"</span>: [<span class="hljs-string">"/path/to/scan.nii.gz"</span>]}).cast_column(<span class="hljs-string">"nifti"</span>, Nifti(decode=<span class="hljs-literal">True</span>)) | |
| img = ds[<span class="hljs-number">0</span>][<span class="hljs-string">"nifti"</span>] <span class="hljs-comment"># instance of: nibabel.nifti1.Nifti1Image</span> | |
| arr = img.get_fdata()<!-- HTML_TAG_END --></pre></div> <p data-svelte-h="svelte-188kxfo">After preparing the dataset you can push it to the Hub:</p> <div class="code-block relative "><div class="absolute top-2.5 right-4"><button class="inline-flex items-center relative text-sm focus:text-green-500 cursor-pointer focus:outline-none transition duration-200 ease-in-out opacity-0 mx-0.5 text-gray-600 " title="code excerpt" type="button"><svg class="" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M28,10V28H10V10H28m0-2H10a2,2,0,0,0-2,2V28a2,2,0,0,0,2,2H28a2,2,0,0,0,2-2V10a2,2,0,0,0-2-2Z" transform="translate(0)"></path><path d="M4,18H2V4A2,2,0,0,1,4,2H18V4H4Z" transform="translate(0)"></path><rect fill="none" width="32" height="32"></rect></svg> <div class="absolute pointer-events-none transition-opacity bg-black text-white py-1 px-2 leading-tight rounded font-normal shadow left-1/2 top-full transform -translate-x-1/2 translate-y-2 opacity-0"><div class="absolute bottom-full left-1/2 transform -translate-x-1/2 w-0 h-0 border-black border-4 border-t-0" style="border-left-color: transparent; border-right-color: transparent; "></div> Copied</div></button></div> <pre class=""><!-- HTML_TAG_START -->ds.push_to_hub(<span class="hljs-string">"<username>/my_nifti_dataset"</span>)<!-- HTML_TAG_END --></pre></div> <p data-svelte-h="svelte-oam80l">This will create a dataset repository containing your NIfTI dataset with a <code>data/</code> folder of parquet shards.</p> <h2 class="relative group"><a id="folder-conventions-and-metadata" class="header-link block pr-1.5 text-lg no-hover:hidden with-hover:absolute with-hover:p-1.5 with-hover:opacity-0 with-hover:group-hover:opacity-100 with-hover:right-full" href="#folder-conventions-and-metadata"><span><svg class="" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" aria-hidden="true" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 256 256"><path d="M167.594 88.393a8.001 8.001 0 0 1 0 11.314l-67.882 67.882a8 8 0 1 1-11.314-11.315l67.882-67.881a8.003 8.003 0 0 1 11.314 0zm-28.287 84.86l-28.284 28.284a40 40 0 0 1-56.567-56.567l28.284-28.284a8 8 0 0 0-11.315-11.315l-28.284 28.284a56 56 0 0 0 79.196 79.197l28.285-28.285a8 8 0 1 0-11.315-11.314zM212.852 43.14a56.002 56.002 0 0 0-79.196 0l-28.284 28.284a8 8 0 1 0 11.314 11.314l28.284-28.284a40 40 0 0 1 56.568 56.567l-28.285 28.285a8 8 0 0 0 11.315 11.314l28.284-28.284a56.065 56.065 0 0 0 0-79.196z" fill="currentColor"></path></svg></span></a> <span>Folder conventions and metadata</span></h2> <p data-svelte-h="svelte-s3ae88">If you organize your dataset in folders you can create splits automatically (train/test/validation) by following a structure like:</p> <div class="code-block relative "><div class="absolute top-2.5 right-4"><button class="inline-flex items-center relative text-sm focus:text-green-500 cursor-pointer focus:outline-none transition duration-200 ease-in-out opacity-0 mx-0.5 text-gray-600 " title="code excerpt" type="button"><svg class="" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M28,10V28H10V10H28m0-2H10a2,2,0,0,0-2,2V28a2,2,0,0,0,2,2H28a2,2,0,0,0,2-2V10a2,2,0,0,0-2-2Z" transform="translate(0)"></path><path d="M4,18H2V4A2,2,0,0,1,4,2H18V4H4Z" transform="translate(0)"></path><rect fill="none" width="32" height="32"></rect></svg> <div class="absolute pointer-events-none transition-opacity bg-black text-white py-1 px-2 leading-tight rounded font-normal shadow left-1/2 top-full transform -translate-x-1/2 translate-y-2 opacity-0"><div class="absolute bottom-full left-1/2 transform -translate-x-1/2 w-0 h-0 border-black border-4 border-t-0" style="border-left-color: transparent; border-right-color: transparent; "></div> Copied</div></button></div> <pre class=""><!-- HTML_TAG_START -->dataset<span class="hljs-regexp">/train/</span>scan_0001.nii | |
| dataset<span class="hljs-regexp">/train/</span>scan_0002.nii | |
| dataset<span class="hljs-regexp">/validation/</span>scan_1001.nii | |
| dataset<span class="hljs-regexp">/test/</span>scan_2001.nii<!-- HTML_TAG_END --></pre></div> <p data-svelte-h="svelte-15ifiur">If you have labels or other metadata, provide a <code>metadata.csv</code>, <code>metadata.jsonl</code>, or <code>metadata.parquet</code> in the folder so files can be linked to metadata rows. The metadata must contain a <code>file_name</code> (or <code>*_file_name</code>) field with the relative path to the NIfTI file next to the metadata file.</p> <p data-svelte-h="svelte-1svw9ic">Example <code>metadata.csv</code>:</p> <div class="code-block relative "><div class="absolute top-2.5 right-4"><button class="inline-flex items-center relative text-sm focus:text-green-500 cursor-pointer focus:outline-none transition duration-200 ease-in-out opacity-0 mx-0.5 text-gray-600 " title="code excerpt" type="button"><svg class="" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M28,10V28H10V10H28m0-2H10a2,2,0,0,0-2,2V28a2,2,0,0,0,2,2H28a2,2,0,0,0,2-2V10a2,2,0,0,0-2-2Z" transform="translate(0)"></path><path d="M4,18H2V4A2,2,0,0,1,4,2H18V4H4Z" transform="translate(0)"></path><rect fill="none" width="32" height="32"></rect></svg> <div class="absolute pointer-events-none transition-opacity bg-black text-white py-1 px-2 leading-tight rounded font-normal shadow left-1/2 top-full transform -translate-x-1/2 translate-y-2 opacity-0"><div class="absolute bottom-full left-1/2 transform -translate-x-1/2 w-0 h-0 border-black border-4 border-t-0" style="border-left-color: transparent; border-right-color: transparent; "></div> Copied</div></button></div> <pre class=""><!-- HTML_TAG_START -->file_name,patient_id,age,diagnosis | |
| scan_0001<span class="hljs-selector-class">.nii</span><span class="hljs-selector-class">.gz</span>,P001,<span class="hljs-number">45</span>,healthy | |
| scan_0002<span class="hljs-selector-class">.nii</span><span class="hljs-selector-class">.gz</span>,P002,<span class="hljs-number">59</span>,disease_x<!-- HTML_TAG_END --></pre></div> <p data-svelte-h="svelte-qnr5el">The <code>Nifti</code> feature works with zipped datasets too — each zip can contain NIfTI files and a metadata file. This is useful when uploading large datasets as archives. | |
| This means your dataset structure could look like this (mixed compressed and uncompressed files):</p> <div class="code-block relative "><div class="absolute top-2.5 right-4"><button class="inline-flex items-center relative text-sm focus:text-green-500 cursor-pointer focus:outline-none transition duration-200 ease-in-out opacity-0 mx-0.5 text-gray-600 " title="code excerpt" type="button"><svg class="" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M28,10V28H10V10H28m0-2H10a2,2,0,0,0-2,2V28a2,2,0,0,0,2,2H28a2,2,0,0,0,2-2V10a2,2,0,0,0-2-2Z" transform="translate(0)"></path><path d="M4,18H2V4A2,2,0,0,1,4,2H18V4H4Z" transform="translate(0)"></path><rect fill="none" width="32" height="32"></rect></svg> <div class="absolute pointer-events-none transition-opacity bg-black text-white py-1 px-2 leading-tight rounded font-normal shadow left-1/2 top-full transform -translate-x-1/2 translate-y-2 opacity-0"><div class="absolute bottom-full left-1/2 transform -translate-x-1/2 w-0 h-0 border-black border-4 border-t-0" style="border-left-color: transparent; border-right-color: transparent; "></div> Copied</div></button></div> <pre class=""><!-- HTML_TAG_START -->dataset<span class="hljs-regexp">/train/</span>scan_0001.nii.gz | |
| dataset<span class="hljs-regexp">/train/</span>scan_0002.nii | |
| dataset<span class="hljs-regexp">/validation/</span>scan_1001.nii.gz | |
| dataset<span class="hljs-regexp">/test/</span>scan_2001.nii<!-- HTML_TAG_END --></pre></div> <h2 class="relative group"><a id="converting-to-pytorch-tensors" class="header-link block pr-1.5 text-lg no-hover:hidden with-hover:absolute with-hover:p-1.5 with-hover:opacity-0 with-hover:group-hover:opacity-100 with-hover:right-full" href="#converting-to-pytorch-tensors"><span><svg class="" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" aria-hidden="true" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 256 256"><path d="M167.594 88.393a8.001 8.001 0 0 1 0 11.314l-67.882 67.882a8 8 0 1 1-11.314-11.315l67.882-67.881a8.003 8.003 0 0 1 11.314 0zm-28.287 84.86l-28.284 28.284a40 40 0 0 1-56.567-56.567l28.284-28.284a8 8 0 0 0-11.315-11.315l-28.284 28.284a56 56 0 0 0 79.196 79.197l28.285-28.285a8 8 0 1 0-11.315-11.314zM212.852 43.14a56.002 56.002 0 0 0-79.196 0l-28.284 28.284a8 8 0 1 0 11.314 11.314l28.284-28.284a40 40 0 0 1 56.568 56.567l-28.285 28.285a8 8 0 0 0 11.315 11.314l28.284-28.284a56.065 56.065 0 0 0 0-79.196z" fill="currentColor"></path></svg></span></a> <span>Converting to PyTorch tensors</span></h2> <p data-svelte-h="svelte-s9a9py">Use the <a href="/docs/datasets/pr_8021/en/package_reference/main_classes#datasets.Dataset.set_transform">set_transform()</a> function to apply the transformation on-the-fly to batches of the dataset:</p> <div class="code-block relative "><div class="absolute top-2.5 right-4"><button class="inline-flex items-center relative text-sm focus:text-green-500 cursor-pointer focus:outline-none transition duration-200 ease-in-out opacity-0 mx-0.5 text-gray-600 " title="code excerpt" type="button"><svg class="" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M28,10V28H10V10H28m0-2H10a2,2,0,0,0-2,2V28a2,2,0,0,0,2,2H28a2,2,0,0,0,2-2V10a2,2,0,0,0-2-2Z" transform="translate(0)"></path><path d="M4,18H2V4A2,2,0,0,1,4,2H18V4H4Z" transform="translate(0)"></path><rect fill="none" width="32" height="32"></rect></svg> <div class="absolute pointer-events-none transition-opacity bg-black text-white py-1 px-2 leading-tight rounded font-normal shadow left-1/2 top-full transform -translate-x-1/2 translate-y-2 opacity-0"><div class="absolute bottom-full left-1/2 transform -translate-x-1/2 w-0 h-0 border-black border-4 border-t-0" style="border-left-color: transparent; border-right-color: transparent; "></div> Copied</div></button></div> <pre class=""><!-- HTML_TAG_START --><span class="hljs-keyword">import</span> torch | |
| <span class="hljs-keyword">import</span> nibabel | |
| <span class="hljs-keyword">import</span> numpy <span class="hljs-keyword">as</span> np | |
| <span class="hljs-keyword">def</span> <span class="hljs-title function_">transform_to_pytorch</span>(<span class="hljs-params">example</span>): | |
| example[<span class="hljs-string">"nifti_torch"</span>] = [torch.tensor(ex.get_fdata()) <span class="hljs-keyword">for</span> ex <span class="hljs-keyword">in</span> example[<span class="hljs-string">"nifti"</span>]] | |
| <span class="hljs-keyword">return</span> example | |
| ds.set_transform(transform_to_pytorch) | |
| <!-- HTML_TAG_END --></pre></div> <p data-svelte-h="svelte-10vkqya">Accessing elements now (e.g. <code>ds[0]</code>) will yield torch tensors in the <code>"nifti_torch"</code> key.</p> <h2 class="relative group"><a id="usage-of-nifti1image" class="header-link block pr-1.5 text-lg no-hover:hidden with-hover:absolute with-hover:p-1.5 with-hover:opacity-0 with-hover:group-hover:opacity-100 with-hover:right-full" href="#usage-of-nifti1image"><span><svg class="" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" aria-hidden="true" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 256 256"><path d="M167.594 88.393a8.001 8.001 0 0 1 0 11.314l-67.882 67.882a8 8 0 1 1-11.314-11.315l67.882-67.881a8.003 8.003 0 0 1 11.314 0zm-28.287 84.86l-28.284 28.284a40 40 0 0 1-56.567-56.567l28.284-28.284a8 8 0 0 0-11.315-11.315l-28.284 28.284a56 56 0 0 0 79.196 79.197l28.285-28.285a8 8 0 1 0-11.315-11.314zM212.852 43.14a56.002 56.002 0 0 0-79.196 0l-28.284 28.284a8 8 0 1 0 11.314 11.314l28.284-28.284a40 40 0 0 1 56.568 56.567l-28.285 28.285a8 8 0 0 0 11.315 11.314l28.284-28.284a56.065 56.065 0 0 0 0-79.196z" fill="currentColor"></path></svg></span></a> <span>Usage of NifTI1Image</span></h2> <p data-svelte-h="svelte-1e5dolb">NifTI is a format to store the result of 3 (or even 4) dimensional brain scans. This includes 3 spatial dimensions (x,y,z) | |
| and optionally a time dimension (t). Furthermore, the given positions here are only relative to the scanner, therefore | |
| the dimensions (4, 5, 6) are used to lift this to real world coordinates.</p> <p data-svelte-h="svelte-2n3p1l">You can visualize nifti files for instance leveraging <code>matplotlib</code> as follows:</p> <div class="code-block relative "><div class="absolute top-2.5 right-4"><button class="inline-flex items-center relative text-sm focus:text-green-500 cursor-pointer focus:outline-none transition duration-200 ease-in-out opacity-0 mx-0.5 text-gray-600 " title="code excerpt" type="button"><svg class="" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M28,10V28H10V10H28m0-2H10a2,2,0,0,0-2,2V28a2,2,0,0,0,2,2H28a2,2,0,0,0,2-2V10a2,2,0,0,0-2-2Z" transform="translate(0)"></path><path d="M4,18H2V4A2,2,0,0,1,4,2H18V4H4Z" transform="translate(0)"></path><rect fill="none" width="32" height="32"></rect></svg> <div class="absolute pointer-events-none transition-opacity bg-black text-white py-1 px-2 leading-tight rounded font-normal shadow left-1/2 top-full transform -translate-x-1/2 translate-y-2 opacity-0"><div class="absolute bottom-full left-1/2 transform -translate-x-1/2 w-0 h-0 border-black border-4 border-t-0" style="border-left-color: transparent; border-right-color: transparent; "></div> Copied</div></button></div> <pre class=""><!-- HTML_TAG_START --><span class="hljs-keyword">import</span> matplotlib.pyplot <span class="hljs-keyword">as</span> plt | |
| <span class="hljs-keyword">from</span> datasets <span class="hljs-keyword">import</span> load_dataset | |
| <span class="hljs-keyword">def</span> <span class="hljs-title function_">show_slices</span>(<span class="hljs-params">slices</span>): | |
| <span class="hljs-string">""" Function to display row of image slices """</span> | |
| fig, axes = plt.subplots(<span class="hljs-number">1</span>, <span class="hljs-built_in">len</span>(slices)) | |
| <span class="hljs-keyword">for</span> i, <span class="hljs-built_in">slice</span> <span class="hljs-keyword">in</span> <span class="hljs-built_in">enumerate</span>(slices): | |
| axes[i].imshow(<span class="hljs-built_in">slice</span>.T, cmap=<span class="hljs-string">"gray"</span>, origin=<span class="hljs-string">"lower"</span>) | |
| nifti_ds = load_dataset(<span class="hljs-string">"<username>/my_nifti_dataset"</span>) | |
| <span class="hljs-keyword">for</span> epi_img <span class="hljs-keyword">in</span> nifti_ds: | |
| nifti_img = epi_img[<span class="hljs-string">"nifti"</span>].get_fdata() | |
| show_slices([nifti_img[:, :, <span class="hljs-number">16</span>], nifti_img[<span class="hljs-number">26</span>, :, :], nifti_img[:, <span class="hljs-number">30</span>, :]]) | |
| plt.show()<!-- HTML_TAG_END --></pre></div> <h2 class="relative group"><a id="for-further-reading-we-refer-to-the-nibabel-documentation-and-especially-this-nibabel-tutorial" class="header-link block pr-1.5 text-lg no-hover:hidden with-hover:absolute with-hover:p-1.5 with-hover:opacity-0 with-hover:group-hover:opacity-100 with-hover:right-full" href="#for-further-reading-we-refer-to-the-nibabel-documentation-and-especially-this-nibabel-tutorial"><span><svg class="" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" aria-hidden="true" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 256 256"><path d="M167.594 88.393a8.001 8.001 0 0 1 0 11.314l-67.882 67.882a8 8 0 1 1-11.314-11.315l67.882-67.881a8.003 8.003 0 0 1 11.314 0zm-28.287 84.86l-28.284 28.284a40 40 0 0 1-56.567-56.567l28.284-28.284a8 8 0 0 0-11.315-11.315l-28.284 28.284a56 56 0 0 0 79.196 79.197l28.285-28.285a8 8 0 1 0-11.315-11.314zM212.852 43.14a56.002 56.002 0 0 0-79.196 0l-28.284 28.284a8 8 0 1 0 11.314 11.314l28.284-28.284a40 40 0 0 1 56.568 56.567l-28.285 28.285a8 8 0 0 0 11.315 11.314l28.284-28.284a56.065 56.065 0 0 0 0-79.196z" fill="currentColor"></path></svg></span></a> <span>For further reading we refer to the nibabel documentation and especially this nibabel tutorial</span></h2> <a class="!text-gray-400 !no-underline text-sm flex items-center not-prose mt-4" href="https://github.com/huggingface/datasets/blob/main/docs/source/nifti_dataset.mdx" target="_blank"><svg class="mr-1" xmlns="http://www.w3.org/2000/svg" aria-hidden="true" fill="currentColor" focusable="false" role="img" width="1em" height="1em" preserveAspectRatio="xMidYMid meet" viewBox="0 0 32 32"><path d="M31,16l-7,7l-1.41-1.41L28.17,16l-5.58-5.59L24,9l7,7z"></path><path d="M1,16l7-7l1.41,1.41L3.83,16l5.58,5.59L8,23l-7-7z"></path><path d="M12.419,25.484L17.639,6.552l1.932,0.518L14.351,26.002z"></path></svg> <span data-svelte-h="svelte-zjs2n5"><span class="underline">Update</span> on GitHub</span></a> <p></p> | |
| <script> | |
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| base: "/docs/datasets/pr_8021/en", | |
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| }; | |
| const element = document.currentScript.parentElement; | |
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