NITRC: mri_reface: help

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Error running mri_reface

When I try to run mri_reface, I get the following error:

$ ./mri_reface ~/Downloads/CT.nii ~/Downloads/ -imType CT
-------------------------------------------------------
Running mri_reface, version 0.3
By: Christopher G. Schwarz schwarz.christopher@mayo.edu
Temp directory: /tmp/tp2b0a7f62_e01f_4f69_a895_b6b21c0d1523
Target file: /home/david/Downloads/CT.nii
Output directory: /home/david/Downloads/
Target image type: CT
Template: /home/david/.mcrCache9.4/mri_re0/images/MCALT_FaceTemplate_CT-PIB.nii
Face atlas: /home/david/.mcrCache9.4/mri_re0/images/MCALT_FaceMask.nii

Calculating affine parameters to template. This will take some time.
Error using ADIR_coreg_to_T1 (line 313)
/home/david/Apps/NiftyReg/bin/reg_aladin -source moving_CT_forCoreg.nii -target fixed_MCALT_FaceTemplate_CT-PIB.nii -aff CT_forCoreg_to_MCALT_FaceTemplate_CT-PIB_AladinAffine.txt -tmask fixed_MCALT_FaceTemplate_CT-PIB_masked_dilatedMask.nii -omp 1failed with output: Err: Parameter -omp unknown.

reg_aladin
Usage: /home/david/Apps/NiftyReg/bin/reg_aladin -ref -flo [OPTIONS].
See the help for more details (-h).

Error in ADIR_ReFace (line 443)

I am using:
NiftyReg Version: 1.3.9
ANTs Version: v2.4.2-g6c72971

It seems that reg_aladin isn't expecting the "-omp" flag. Is there a different version of NiftyReg that I should be using?

Thanks,
David

Error running mri_reface

David,
You will want to compile niftyreg version 1.5 or better. Their github is he=
re https://github.com/KCL-BMEIS/niftyreg. It may be possible to get around =
the omp requirement, but failure rates with 1.3.x will be higher than with =
1.5.x.
Chris Schwarz

RE: Error running mri_reface

Hello Chris,

Thank you for your help! I was able to build a docker image that could run mri_reface, though, it returns an error when trying to generate the face renderings. It seems like there is a problem with using matlab runtime. But I don't really care about the face renderings, so I've given up on debugging it.

I've attached the Dockerfile I created in case anyone is interested in using it. It is designed to be built within the mri_reface folder.

Thanks again,
David

Attachment: Dockerfile

RE: Error running mri_reface

David,
I'm glad you got it mostly working, although I can't seem to view your attachment. When I click the attachment, Nitrc opens a window with nothing in it but a button to close the window, and some unrelated information. Are you able to view/download your own attachment? I'm trying to figure out if the problem is with nitrc software, my downloading, or your uploading.
Thanks,
Chris

RE: Error running mri_reface

Hello Chris,

I cannot access my own attachment either. I went ahead and made a GitHub repository with the Dockerfile in it here:
https://github.com/ellisdg/mri_reface_dockerfile

Best,
David

RE: Error running mri_reface

Hi (on behalf of NITRC),

This does appear to be an issue with NITRC, and we're looking into it.

Until then, I've posted the data below.

# Use Ubuntu 22.04 LTS
FROM ubuntu:22.04

ENV DEBIAN_FRONTEND="noninteractive" \
LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8"

RUN apt-get update && \
apt-get install -y --no-install-recommends \
apt-utils \
autoconf \
build-essential \
bzip2 \
ca-certificates \
curl \
git \
libtool \
lsb-release \
netbase \
pkg-config \
xorg \
unzip \
wget \
cmake \
make \
xvfb && \
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Installing ANTs 2.3.3 (NeuroDocker build)
# Note: the URL says 2.3.4 but it is actually 2.3.3
ENV ANTSPATH="/opt/ants" \
PATH="/opt/ants:$PATH"
WORKDIR $ANTSPATH
RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
| tar -xzC $ANTSPATH --strip-components 1

# Installing niftyreg
WORKDIR "/opt"
RUN git clone https://github.com/KCL-BMEIS/niftyreg.gi...
RUN mkdir niftyreg-build
RUN cd ./niftyreg-build && cmake ../niftyreg && make

# setup niftyreg
RUN rm -rf ./niftyreg && mv ./niftyreg-build /opt/niftyreg
ENV PATH="/opt/niftyreg/reg-io:/opt/niftyreg/reg-apps:$PATH"

# Install matlab-runtime
# Modified from https://github.com/dafnifacility/matlab-...
# Install pre-requisites
RUN mkdir -p /matlab-runtime /opt/matlab-runtime/v94/archives /code/model

# Download and install Matlab runtime
RUN wget https://ssd.mathworks.com/supportfiles/d... && \
unzip MCR_R2018a_glnxa64_installer.zip && \
rm -rf MCR_R2018a_glnxa64_installer.zip && \
./install -destinationFolder /opt/matlab-runtime -agreeToLicense yes -mode silent -outputFile /log.txt $$ \
rm -rf /matlab-runtime
ENV MCRROOT=/opt/matlab-runtime/v94

# Point to the newly installed Matlab runtime binaries
ENV LD_LIBRARY_PATH $MCRROOT:$MCRROOT/runtime/glnxa64:$MCRROOT/bin/glnxa64:$MCRROOT/sys/os/glnxa64:$MCRROOT/sys/opengl/lib/glnxa64:$MCRROOT/extern/bin/glnxa64

# Add mri_reface
COPY * /opt/mri_reface/
ENV PATH="/opt/mri_reface:$PATH"

WORKDIR "/home"

RE: Error running mri_reface

Thanks for sharing! We do plan to do this officially someday but there are a lot of competing priorities. Your version can help others in the meantime.

RE: Error running mri_reface

Thanks for looking into it, NITRC team!

RE: Error running mri_reface

David,

You may be interested in our new 0.3.2 release, which now has an officially supported Docker image. It took a while, but we found a way around the remder/openGL errors inside Docker. We had to create the Docker image using Matlab's own tools during the initial compile of mri_reface, and then amend that Matlab-created Dockerfile with our additional dependencies. Matlab seems to do something special with the Matlab runtime in the Docker images that it creates.

Chris

RE: Error running mri_reface

Chris,

Thanks for letting me know!

David