neurodata/fsl_1604 repository overview

⁠Documentation

The software contained in this docker container is the FSL 5.0.7 installation built from debian. For details on FSL, please see the FSL website⁠. For the installed FSL package, please see debian FSL⁠.

⁠Acknowledgments

When using this software, please find the respective package you are using from the FSL wiki⁠, and use the appropriate citation recommended by the FSL team.

⁠Instructions

In your terminal window, type:

$ docker pull neurodata/fsl_1604

Like a normal docker container, we can start our container with a single line. We can start the container by typing:

$ docker run -ti --entrypoint /bin/bash -v <desired-host-path>:<desired-docker-path> neurodata/fsl_1604
# <desired-host-path>: the path to a local directory you want to process data on
# <desired-docker-path>: the path in which your local data will be accessible

You can then use all of the standard FSL functions from inside of the container.

⁠Example

In this example, we will demonstrate a simple use of the FSL utilities on a single brain. To accomplish this, we will download a single anatomical image, skullstrip it, and then look at the result. To verify that FSL worked properly, you can install the mricron⁠ nifti viewer, or use your favorite nifti image viewer.

First, switch to your local downloads folder, and obtain the following T1w anatomical image:

cd ~/Downloads
wget http://openconnecto.me/mrdata/share/demo_data/sub-0025864_ses-1_T1w.nii.gz

This image can be visualized as follows:

mricron sub-0025864_ses-1_T1w.nii.gz

As we can see, the image is a high-resolution anatomical T1w scan, with a skull-on.

Next, pull the FSL 16.04 image locally:

docker pull neurodata/fsl_1604

Once the pull completes, enter the container and pass the appropriate directory:

docker run -ti --entrypoint /bin/bash -v ~/Downloads:/data neurodata/fsl_1604

Finally, run the algorithm:

bet /data/sub-0025864_ses-1_T1w.nii.gz /data/sub-0025864_ses-1_T1w_brain.nii.gz

Locally, navigate back to your downloads folder, and you should see the produced image, and be able to visualize it:

cd ~/Downloads
mricron sub-0025864_ses-1_T1w_brain.nii.gz

Note that the image has had its skull removed compared to what we previously visualized.

⁠Error Reporting

If you find any errors with this docker container or have any questions, feel free to open an issue⁠.