MREG analysis part 2: preprocessing

Cheaha

Connect to your CHEAHA account:

  • Go to https://rc.uab.edu/ and login

  • Click on My interactive session on top

  • Click on HPC Desktop (If no session was previously created)

  • Create a new session with following options: chose what you need

  • Click on Launch desktop in new Tab

  • Hurray, you are now in your own Linux session on CHEAHA!

Getting docker image

  • All the toolbox and packages analysis you need have been put into a Docker image (yeah!)

  • Unfortunately, CHEAHA does not support Docker. However, we can use Singularity which is pretty much the same.

  • First let’s load Singularity on Cheaha. Open a terminal and type:

module load Singularity

  • Next let’s convert the Docker image and put it in a folder of your choice (change /path/to/ ):

singularity build /path/to/singularity/NIPYPE_docker.simg docker://orchid666/myneurodocker:NIPYPE

  • You are now ready to preprocess your images!!

Launching docker session

  • You are now ready to preprocess your MREG images

  • Let’s go to where you put the Singularity image:

cd /path/to/singularity/

  • Now let’s launch the Docker session and tell it where your stuff is:

singularity shell –bind /Mreg_analysis:/data –bind /path/to/scripts:/myscripts NIPYPE_docker.simg source activate neuro