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| Robust, universal skull-stripping for brain images of any type. <<BR>> {{attachment:skullstrips.png||height="250"}} <<BR>> Note: this functionality is currently only available in the development version of !FreeSurfer. Rather than directly contacting the author, please post your questions on this module to the !FreeSurfer [[FreeSurferSupport|mailing list]]. |
'''''Robust, universal brain-extraction for images of any type.''''' |
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| This wiki page is still a work-in-progress. | {{attachment:skullstrips.png||width="600"}} SynthStrip is a skull-stripping tool that accurately extracts brain signal from a landscape of image types, ranging across imaging modality, contrast, resolution, and subject population. It leverages a deep-learning strategy that synthesizes arbitrary training images from segmentation maps to optimize a robust model agnostic to acquisition specifics. If you use !SynthStrip in your analysis, please cite: '''SynthStrip: Skull-Stripping for Any Brain Image'''<<BR>> Andrew Hoopes, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl, Malte Hoffmann.<<BR>> [[https://arxiv.org/abs/2203.09974|arXiv preprint]]. '''Note:''' If you have questions related to running SynthStrip, please post your issue to the !FreeSurfer [[FreeSurferSupport|mailing list]] instead of reaching out directly to the authors. |
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| We offer two ways of running !SynthStrip: within !FreeSurfer or as a standalone command-line tool. | The !SynthStrip command line tool can be be run within !FreeSurfer or as standalone utility using Docker or Singularity containers. |
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| '''''Within !FreeSurfer:''''' As of March 14 2022, SynthStrip is available in the dev (nightly) !FreeSurfer distributions and will be included in the upcoming !FreeSurfer v7.3 release. | '''Within !FreeSurfer:''' As of March 16 2022, the `mri_synthstrip` command is available in the dev (nightly) !FreeSurfer distributions and will be included in the upcoming !FreeSurfer v7.3 release. |
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| '''''Standalone Utility:''''' Coming soon! /* If you do not want to install an entire !FreeSurfer distribution to run !SynthStrip, you can install a singular, pre-built macOS or linux !SynthStrip executable. To do this, download the maxOS or linux file from this source. */ | If you do not want to install an entire !FreeSurfer distribution, you can run !SynthStrip through a standalone script that wraps either a Docker or Singularity container. To download either of these scripts, run the commands described below. Once downloaded, please read the brief instructions in the header of the downloaded script. This is especially necessary for the Singularity script, which requires setting up a one-time configuration. The downloaded scripts can be run directly, using the same command-line syntax defined in the ''Usage'' section below. '''Singularity:''' To download the Singularity-based wrapper script, run: {{{ curl -O https://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/synthstrip/synthstrip-singularity && chmod +x synthstrip-singularity }}} '''Docker:''' To download the Docker-based wrapper script, run: {{{ curl -O https://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/synthstrip/synthstrip-docker && chmod +x synthstrip-docker }}} The aim of these wrappers is to provide easy mechanisms for running SynthStrip containers, i.e. so users do not need to worry about mounting paths to input and output files, etc. For those interested, the underlying build image can be accessed from [[https://hub.docker.com/r/freesurfer/synthstrip|DockerHub]]. |
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| Once installed, you can run !SynthStrip with the following: | Once installed, you can run !SynthStrip with the following command-line syntax: |
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| synthstrip -i <input> -o <stripped> | mri_synthstrip -i <input> -o <stripped> |
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| In this command, `<input>` represents the path to the input image and `<stripped>` is the skull-stripped output. To also save the corresponding brain mask, the `-m` command line flag can be used to specify the mask output path. For additional options and command description, please use the `--help` flag. For the large majority of images with voxel sizes near 1 mm^3, !SynthStrip should run in less than 1 minute on the CPU. As image size (or resolution) increases, this runtime might increase as well. | '''Note:''' If using the Docker or Singularity wrappers, replace `mri_synthstrip` with the downloaded script name, e.g. `synthstrip-singularity`. In this command, `<input>` represents the path to the input image and `<stripped>` is the skull-stripped output. To also save the corresponding brain mask, the `-m` command line flag can be used to specify the mask output path. For additional options and command description, please use the `--help` flag. For the large majority of images with voxel sizes near 1 mm^3^, !SynthStrip should run in less than 1 minute on the CPU. As image size (or resolution) increases, this runtime might increase as well. |
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| In the SynthStrip publication, we gather a large test set, from a collection of public datasets, that spans across acquisition type, age, and health. We plan to make this subset of images, along with ground-truth brain mask labels, available for download in the near future. | In the SynthStrip publication, we gather a test collection of public datasets that span across acquisition type and subject population. We make this subset of images, with ground-truth brain mask labels, available for download as a [[https://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/synthstrip/synthstrip_data_v1.tar.gz|compressed tar archive]]. Note that we only distribute images from datasets that we have permission for. A breakdown of the datasets is available in the README of the archive, and please be sure to cite SynthStrip and the relevant work (more details in the README) if you use any of this data in a publication. == 5. Code == Open-source code is available in the !FreeSurfer !GitHub repository, at https://github.com/freesurfer/freesurfer/tree/dev/mri_synthstrip. |
SynthStrip
Robust, universal brain-extraction for images of any type.
1. Overview
SynthStrip is a skull-stripping tool that accurately extracts brain signal from a landscape of image types, ranging across imaging modality, contrast, resolution, and subject population. It leverages a deep-learning strategy that synthesizes arbitrary training images from segmentation maps to optimize a robust model agnostic to acquisition specifics.
If you use SynthStrip in your analysis, please cite:
SynthStrip: Skull-Stripping for Any Brain Image
Andrew Hoopes, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl, Malte Hoffmann.
arXiv preprint.
Note: If you have questions related to running SynthStrip, please post your issue to the FreeSurfer mailing list instead of reaching out directly to the authors.
2. Installation
The SynthStrip command line tool can be be run within FreeSurfer or as standalone utility using Docker or Singularity containers.
Within FreeSurfer: As of March 16 2022, the mri_synthstrip command is available in the dev (nightly) FreeSurfer distributions and will be included in the upcoming FreeSurfer v7.3 release.
If you do not want to install an entire FreeSurfer distribution, you can run SynthStrip through a standalone script that wraps either a Docker or Singularity container. To download either of these scripts, run the commands described below. Once downloaded, please read the brief instructions in the header of the downloaded script. This is especially necessary for the Singularity script, which requires setting up a one-time configuration. The downloaded scripts can be run directly, using the same command-line syntax defined in the Usage section below.
Singularity: To download the Singularity-based wrapper script, run:
curl -O https://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/synthstrip/synthstrip-singularity && chmod +x synthstrip-singularity
Docker: To download the Docker-based wrapper script, run:
curl -O https://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/synthstrip/synthstrip-docker && chmod +x synthstrip-docker
The aim of these wrappers is to provide easy mechanisms for running SynthStrip containers, i.e. so users do not need to worry about mounting paths to input and output files, etc. For those interested, the underlying build image can be accessed from DockerHub.
3. Usage
Once installed, you can run SynthStrip with the following command-line syntax:
mri_synthstrip -i <input> -o <stripped>
Note: If using the Docker or Singularity wrappers, replace mri_synthstrip with the downloaded script name, e.g. synthstrip-singularity.
In this command, <input> represents the path to the input image and <stripped> is the skull-stripped output. To also save the corresponding brain mask, the -m command line flag can be used to specify the mask output path. For additional options and command description, please use the --help flag. For the large majority of images with voxel sizes near 1 mm3, SynthStrip should run in less than 1 minute on the CPU. As image size (or resolution) increases, this runtime might increase as well.
4. Evaluation Dataset
In the SynthStrip publication, we gather a test collection of public datasets that span across acquisition type and subject population. We make this subset of images, with ground-truth brain mask labels, available for download as a compressed tar archive. Note that we only distribute images from datasets that we have permission for. A breakdown of the datasets is available in the README of the archive, and please be sure to cite SynthStrip and the relevant work (more details in the README) if you use any of this data in a publication.
5. Code
Open-source code is available in the FreeSurfer GitHub repository, at https://github.com/freesurfer/freesurfer/tree/dev/mri_synthstrip.