Re: [Freesurfer] synthstrip use as a Docker for all MRI files in directory

Hi Ivan,

Thank you for your interest in SynthStrip. A Dockerfile is only executed once, when you build ("compile") the container, not when you run it. You may want to consider writing a simple Python or shell script that loops over your files and calls the existing container on each.

Do you have the SynthStrip container set up and running?

Malte

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sanchez Fernandez, Ivan Ivan.SanchezFernandez@childrens.harvard.edu Sent: Thursday, April 3, 2025 22:11 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] synthstrip use as a Docker for all MRI files in directory

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First of all, thank you for developing freesurfer and synthstrip. They are wonderful tools.

I am doing research with brain MRIs and part of the preprocessing needs skull stripping. Synthstrip is great.

What I am trying to do is to create a Docker image that runs through all the MRI files in a directory and skull strips them with synthstrip. I thought this would be easy. My multistage Dockerfile looks like this, but it does not work because it does not recognize the command in the loop freesurfer/synthstrip -i "$file" -o "$file" or mri_synthstrip -i "$file" -o "$file" I guess that I do not know how to call a particular command within a unix loop.

#########STAGE 1: CREATE THE MOUNT AND COPY THE MRIs TO BE SKULL-STRIPPED#########

# Use ubuntu as base image FROM ubuntu AS prepare

# Set working directory WORKDIR /app

# Copy all MRIs COPY . .

#########STAGE 2: USE SYNTHSTRIP######### FROM freesurfer/synthstrip

# Set working directory WORKDIR /app

# Copy all MRIs COPY --from=prepare . .

# Create a loop that runs through the MRIs RUN for file in .; do freesurfer/synthstrip -i "$file" -o "$file"; done

ENTRYPOINT ["ls"]

Other option I thought about is to create a multistage build in which first I import the synthstrip program and then I loop through the MRI files and call synthstrip, but again I do not know exactly how to call the command to run synthstrip from python. Dockerfile

#########STAGE 1: CREATE THE SYNTHSTRIP CONTAINER###########

# Use synthstrip AS base image FROM freesurfer/synthstrip as builder

# Set working directory WORKDIR /app

#########STAGE 2: CREATE THE ANACONDA CONTAINER###########

# Use miniconda as base image FROM continuumio/miniconda3

# Set working directory WORKDIR /app

# Copy the initial image COPY --from=builder . .

# Create the environment COPY environment.yml . RUN conda env create -f environment.yml

# Make run commands use the new environment SHELL ["conda", "run", "-n", "app", "bin/bash", "-c"]

# Code to run when the container is started COPY main.py . ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "app", "python", "main.py"]

main.py file

import os import subprocess

for MRI in os.listdir('./file_with_MRIs'): print(MRI) proc = subprocess.Popen(['docker run freesurfer/synthstrip -i ', MRI, ' -o', MRI], stdin = subprocess.PIPE, stdout = subprocess.PIPE, stderr = subprocess.PIPE )

(out, err) = proc.communicate() print (out)

Other option is to create a smaller Docker image that loops through the MRI files and just calls the synthstrip Docker image for each of those and collects the output, but I am not sure how to do that. Any suggestion or guidance highly appreciated. Thank you very much