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This guide describes how to build and run containers to execute and examine the outputs of FreeSurfer's infant pipeline. == Overview == [https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS FreeSurfer's infant pipeline] provides morphological (both volumetric and surface-based) analyses of human neuroanatomy from MRI scans of subjects that are between 0 and 24 months old. The input to the pipeline is an T1-weighted MRI image that has been optimized to maximize the contrast between grey matter, white matter and cerebral spinal fluid (CSF). See [https://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf this document] for guidance on how to configure your MRI scanner to generate these images. The output of the pipeline is a volumetric and surface-based analysis and can be viewed with [https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/ FreeView]. In order to increase reproducibility and make the pipeline easier to use, we have packaged it into ''containers''. A container is a standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another. We have also extended the open source tool [https://www.repronim.org/neurodocker/ neurodocker] to support the creation of FreeSurfer containers from source, facilitating ''continuous integration'' (automated test workflows for each software change) of the infant pipeline. Finally, we leverage the open source tool [https://www.neurodesk.org/ neurodesk] to run FreeSurfer's Freeview and inspect the outputs of the pipeline. |
Containers for running FreeSurfer's infant pipeline
This guide describes how to build and run containers to execute and examine the outputs of FreeSurfer's infant pipeline.
Overview
[https://surfer.nmr.mgh.harvard.edu/fswiki/infantFS FreeSurfer's infant pipeline] provides morphological (both volumetric and surface-based) analyses of human neuroanatomy from MRI scans of subjects that are between 0 and 24 months old.
The input to the pipeline is an T1-weighted MRI image that has been optimized to maximize the contrast between grey matter, white matter and cerebral spinal fluid (CSF). See [https://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf this document] for guidance on how to configure your MRI scanner to generate these images.
The output of the pipeline is a volumetric and surface-based analysis and can be viewed with [https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/ FreeView].
In order to increase reproducibility and make the pipeline easier to use, we have packaged it into containers. A container is a standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another.
We have also extended the open source tool [https://www.repronim.org/neurodocker/ neurodocker] to support the creation of FreeSurfer containers from source, facilitating continuous integration (automated test workflows for each software change) of the infant pipeline.
Finally, we leverage the open source tool [https://www.neurodesk.org/ neurodesk] to run FreeSurfer's Freeview and inspect the outputs of the pipeline.