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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
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