The Dockerfile is missing installation of dwidenoise from Mrtrix3 to run the dwi workflow

celprov commented 10 months ago

What happened?

I built the singularity image from the Dockerfile as it currently is in nipreps/mriqc:master and tried to run it on our dense-sampling dataset containing DWI images.

But that image is missing the installation of dwidenoise to run the dwi workflow of MRIQC. dwidenoise is a package from mrtrix3.

The Dockerfile thus needs to be adapted to include this package.

What command did you use?

docker build \
-t local/mriqc:latest \
--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
--build-arg VCS_REF=`git rev-parse --short HEAD` \
--build-arg VERSION="23.2.0" /data/code/mriqc

docker run --privileged -t --rm \
    -v /var/run/docker.sock:/var/run/docker.sock \
    -v /absolute/path/to/output/folder:/output \
    singularityware/docker2singularity \
    local/mriqc:latest

singularity run -e -B $DATADIR:/data:ro \
-B ${WORKDIR}:/work \
-B ${OUTDIR}:/out \ 
/oak/stanford/groups/russpold/users/cprovins/singularity_images/local-mriqc-23.2.0.simg \
/data /out participant \
-w /work --session-id ${SES#ses-} \
--verbose-reports --nprocs 4 --mem 40G --omp-nthreads 8 -vv

What version of the software are you running?

nipreps/mriqc:master

How are you running this software?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node dwidenoise.

Cmdline:
    dwidenoise -mask /work/mriqc_wf/dwiMRIQC/synthstrip_wf/_in_file_..data..sub-001..ses-001..dwi..sub-001_ses-001_acq-highres_dir-LR_dwi.nii.gz/synthstrip/clipped_corrected_desc-brain_mask.nii.gz -noise noisemap.nii.gz -nthreads 8 /work/mriqc_wf/dwiMRIQC/_in_file_..data..sub-001..ses-001..dwi..sub-001_ses-001_acq-highres_dir-LR_dwi.nii.gz/dti_filter/sub-001_ses-001_acq-highres_dir-LR_dwi_valid_nodriftfull_dti.nii.gz sub-001_ses-001_acq-highres_dir-LR_dwi_valid_nodriftfull_dti_denoised.nii.gz
Stdout:

Stderr:

Traceback:
    Traceback (most recent call last):
      File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 397, in run
        runtime = self._run_interface(runtime)
      File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 752, in _run_interface
        raise IOError(
    OSError: No command "dwidenoise" found on host sh02-06n01.int. Please check that the corresponding package is installed.

Additional information / screenshots

No response

effigies commented 10 months ago

https://www.mrtrix.org/download/linux-anaconda/

Install mrtrix3 from the mrtrix3 channel.

conda install -c mrtrix3 mrtrix3

effigies commented 10 months ago

Installing on its own has a lot of dependencies

``` ❯ mamba create -n mrtrix3 -c mrtrix3 mrtrix3 Looking for: ['mrtrix3'] mrtrix3/linux-64 (check zst) Checked 0.2s mrtrix3/noarch (check zst) Checked 0.1s conda-forge/linux-64 Using cache conda-forge/noarch Using cache pkgs/main/linux-64 Using cache pkgs/main/noarch Using cache pkgs/r/linux-64 Using cache pkgs/r/noarch Using cache mrtrix3/noarch 116.0 B @ 455.0 B/s 0.3s mrtrix3/linux-64 797.0 B @ 1.8kB/s 0.4s Transaction Prefix: /home/chris/mambaforge/envs/mrtrix3 Updating specs: - mrtrix3 Package Version Build Channel Size ───────────────────────────────────────────────────────────────────────────────────────── Install: ───────────────────────────────────────────────────────────────────────────────────────── + _libgcc_mutex 0.1 conda_forge conda-forge Cached + libstdcxx-ng 13.2.0 h7e041cc_4 conda-forge Cached + ca-certificates 2023.11.17 hbcca054_0 conda-forge Cached + ld_impl_linux-64 2.40 h41732ed_0 conda-forge Cached + libgomp 13.2.0 h807b86a_4 conda-forge 422kB + _openmp_mutex 4.5 2_gnu conda-forge Cached + libgcc-ng 13.2.0 h807b86a_4 conda-forge Cached + xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge Cached + xorg-kbproto 1.0.7 h7f98852_1002 conda-forge Cached + xorg-xproto 7.0.31 h7f98852_1007 conda-forge Cached + xorg-damageproto 1.2.1 h7f98852_1002 conda-forge 25kB + xorg-renderproto 0.11.1 h7f98852_1002 conda-forge Cached + xorg-randrproto 1.5.0 h7f98852_1001 conda-forge 33kB + xorg-recordproto 1.14.2 h7f98852_1002 conda-forge 8kB + xorg-inputproto 2.3.2 h7f98852_1002 conda-forge 20kB + graphite2 1.3.13 h58526e2_1001 conda-forge Cached + xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge Cached + pthread-stubs 0.4 h36c2ea0_1001 conda-forge Cached + libxcrypt 4.4.36 hd590300_1 conda-forge Cached + ncurses 6.4 h59595ed_2 conda-forge Cached + xorg-compositeproto 0.4.2 h7f98852_1001 conda-forge 12kB + libnsl 2.0.1 hd590300_0 conda-forge Cached + attr 2.5.1 h166bdaf_1 conda-forge Cached + mpg123 1.32.4 h59595ed_0 conda-forge Cached + libogg 1.3.4 h7f98852_1 conda-forge Cached + lame 3.100 h166bdaf_1003 conda-forge Cached + lz4-c 1.9.4 hcb278e6_0 conda-forge Cached + libopus 1.3.1 h7f98852_1 conda-forge Cached + xorg-util-macros 1.19.3 h7f98852_0 conda-forge 52kB + xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge Cached + pixman 0.43.2 h59595ed_0 conda-forge 387kB + openssl 3.2.0 hd590300_1 conda-forge Cached + libiconv 1.17 hd590300_2 conda-forge Cached + libffi 3.4.2 h7f98852_5 conda-forge Cached + giflib 5.2.1 h0b41bf4_3 conda-forge Cached + xorg-libxau 1.0.11 hd590300_0 conda-forge Cached + bzip2 1.0.8 hd590300_5 conda-forge Cached + keyutils 1.6.1 h166bdaf_0 conda-forge Cached + libuuid 2.38.1 h0b41bf4_0 conda-forge Cached + xorg-libice 1.1.1 hd590300_0 conda-forge Cached + gettext 0.21.1 h27087fc_0 conda-forge Cached + icu 73.2 h59595ed_0 conda-forge Cached + nspr 4.35 h27087fc_0 conda-forge Cached + libexpat 2.5.0 hcb278e6_1 conda-forge Cached + alsa-lib 1.2.10 hd590300_0 conda-forge Cached + libgfortran5 13.2.0 ha4646dd_4 conda-forge Cached + libjpeg-turbo 3.0.0 hd590300_1 conda-forge Cached + libzlib 1.2.13 hd590300_5 conda-forge Cached + libwebp-base 1.3.2 hd590300_0 conda-forge Cached + libdeflate 1.19 hd590300_0 conda-forge Cached + xz 5.2.6 h166bdaf_0 conda-forge Cached + lerc 4.0.0 h27087fc_0 conda-forge Cached + libedit 3.1.20191231 he28a2e2_2 conda-forge Cached + readline 8.2 h8228510_1 conda-forge Cached + libcap 2.69 h0f662aa_0 conda-forge Cached + libvorbis 1.3.7 h9c3ff4c_0 conda-forge Cached + xorg-fixesproto 5.0 h7f98852_1002 conda-forge Cached + mysql-common 8.0.33 hf1915f5_6 conda-forge Cached + libevent 2.1.12 hf998b51_1 conda-forge Cached + libxcb 1.15 h0b41bf4_0 conda-forge Cached + xorg-libsm 1.2.4 h7391055_0 conda-forge Cached + libgpg-error 1.47 h71f35ed_0 conda-forge Cached + libflac 1.4.3 h59595ed_0 conda-forge Cached + expat 2.5.0 hcb278e6_1 conda-forge Cached + libgfortran-ng 13.2.0 h69a702a_4 conda-forge Cached + tk 8.6.13 noxft_h4845f30_101 conda-forge Cached + pcre2 10.42 hcad00b1_0 conda-forge Cached + libsqlite 3.44.2 h2797004_0 conda-forge Cached + libpng 1.6.39 h753d276_0 conda-forge Cached + zlib 1.2.13 hd590300_5 conda-forge Cached + zstd 1.5.5 hfc55251_0 conda-forge Cached + libxml2 2.12.4 h232c23b_1 conda-forge Cached + krb5 1.21.2 h659d440_0 conda-forge Cached + xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge Cached + xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge Cached + xcb-util 0.4.0 hd590300_1 conda-forge Cached + xcb-util-renderutil 0.3.9 hd590300_1 conda-forge Cached + xorg-libx11 1.8.7 h8ee46fc_0 conda-forge Cached + libgcrypt 1.10.3 hd590300_0 conda-forge Cached + libsndfile 1.2.2 hc60ed4a_1 conda-forge Cached + fftw 3.3.10 nompi_hc118613_108 conda-forge Cached + libglib 2.78.3 h783c2da_0 conda-forge Cached + nss 3.97 h1d7d5a4_0 conda-forge Cached + freetype 2.12.1 h267a509_2 conda-forge Cached + mysql-libs 8.0.33 hca2cd23_6 conda-forge Cached + libtiff 4.6.0 ha9c0a0a_2 conda-forge Cached + libllvm15 15.0.7 hb3ce162_4 conda-forge Cached + libpq 16.1 h33b98f1_7 conda-forge Cached + libcups 2.3.3 h4637d8d_4 conda-forge Cached + xcb-util-image 0.4.0 h8ee46fc_1 conda-forge Cached + xkeyboard-config 2.40 hd590300_0 conda-forge Cached + xorg-libxext 1.3.4 h0b41bf4_2 conda-forge Cached + xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge Cached + xorg-libxrender 0.9.11 hd590300_0 conda-forge Cached + libsystemd0 255 h3516f8a_0 conda-forge Cached + glib-tools 2.78.3 hfc55251_0 conda-forge Cached + dbus 1.13.6 h5008d03_3 conda-forge Cached + fontconfig 2.14.2 h14ed4e7_0 conda-forge Cached + libwebp 1.3.2 h658648e_1 conda-forge Cached + libclang13 15.0.7 default_ha2b6cf4_4 conda-forge Cached + libxkbcommon 1.6.0 hd429924_1 conda-forge Cached + xorg-libxcomposite 0.4.6 h0b41bf4_1 conda-forge 13kB + xorg-libxi 1.7.10 h7f98852_0 conda-forge 47kB + xorg-libxdamage 1.1.5 h7f98852_1 conda-forge 12kB + xorg-libxrandr 1.5.2 h7f98852_1 conda-forge 30kB + pulseaudio-client 16.1 hb77b528_5 conda-forge Cached + libclang 15.0.7 default_hb11cfb5_4 conda-forge Cached + xorg-libxtst 1.2.3 h7f98852_1002 conda-forge 32kB + font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge Cached + font-ttf-inconsolata 3.000 h77eed37_0 conda-forge Cached + font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge Cached + font-ttf-ubuntu 0.83 h77eed37_1 conda-forge Cached + tzdata 2023d h0c530f3_0 conda-forge Cached + fonts-conda-forge 1 0 conda-forge Cached + fonts-conda-ecosystem 1 0 conda-forge Cached + python 3.12.1 hab00c5b_1_cpython conda-forge Cached + cairo 1.18.0 h3faef2a_0 conda-forge Cached + harfbuzz 8.3.0 h3d44ed6_0 conda-forge Cached + wheel 0.42.0 pyhd8ed1ab_0 conda-forge Cached + setuptools 69.0.3 pyhd8ed1ab_0 conda-forge Cached + pip 23.3.2 pyhd8ed1ab_0 conda-forge Cached + glib 2.78.3 hfc55251_0 conda-forge Cached + gstreamer 1.22.9 h98fc4e7_0 conda-forge Cached + gst-plugins-base 1.22.9 h8e1006c_0 conda-forge Cached + qt-main 5.15.8 h450f30e_18 conda-forge Cached + qt-webengine 5.15.8 h7517aa4_5 conda-forge 58MB + qt 5.15.8 hf11cfaa_0 conda-forge 17kB + mrtrix3 3.0.4 h2bc3f7f_0 mrtrix3 21MB Summary: Install: 128 packages Total download: 81MB ───────────────────────────────────────────────────────────────────────────────────────── Confirm changes: [Y/n] y xorg-randrproto 33.0kB @ 193.2kB/s 0.2s xorg-recordproto 8.0kB @ 45.6kB/s 0.2s xorg-inputproto 19.6kB @ 111.6kB/s 0.2s xorg-damageproto 25.4kB @ 119.2kB/s 0.2s xorg-libxdamage 12.0kB @ 50.2kB/s 0.1s qt 17.1kB @ 66.9kB/s 0.1s xorg-libxcomposite 13.4kB @ 44.0kB/s 0.1s xorg-libxtst 32.1kB @ 103.7kB/s 0.1s xorg-util-macros 52.5kB @ 157.0kB/s 0.1s libgomp 422.1kB @ 1.3MB/s 0.3s xorg-libxrandr 29.7kB @ 77.1kB/s 0.1s xorg-libxi 47.3kB @ 113.5kB/s 0.1s xorg-compositeproto 12.4kB @ 24.9kB/s 0.1s pixman 386.8kB @ 737.1kB/s 0.2s mrtrix3 21.1MB @ 7.6MB/s 2.5s qt-webengine 58.4MB @ 17.8MB/s 3.1s Downloading and Extracting Packages: Preparing transaction: done Verifying transaction: done Executing transaction: done To activate this environment, use $ mamba activate mrtrix3 To deactivate an active environment, use $ mamba deactivate ```

That's a lot of potential conflicts. We could do a build stage where we install and then copy, but maybe instead it makes sense to copy from their docker image: https://hub.docker.com/r/mrtrix3/mrtrix3/tags

# Tested, and we need at least these libraries to run dwidenoise --help
RUN apt update && apt install --no-install-recommends -y libtiff5 libpng16-16

copy --from=mrtrix3/mrtrix3:3.0.4 /opt/mrtrix3/bin/dwidenoise /usr/local/bin
copy --from=mrtrix3/mrtrix3:3.0.4 /opt/mrtrix3/lib/libmrtrix.so /usr/local/lib

nipreps / mriqc