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mridefacer fix and update
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This commit and PR fixes and updates mridefacer, as it crashed based on inconsistencies in the respective function's setup. 
The following files were changed:

- generate_iamges.sh & Dockerfile -> FSL templates were added to the container as they are needed by mridefacer
- defacing_algorithms -> mridefacer commands and workflow were updated to remove problems wrt copying of the face mask & add the --outdir argument to write defaced images to the respective BIDS root directory
- run_deeid -> updated to reflect the changes made in defacing_algorithms
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@PeerHerholz
PeerHerholz committed Jun 7, 2021
1 parent 61d389e commit 5ddcc42
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Showing 4 changed files with 131 additions and 19 deletions.
123 changes: 121 additions & 2 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# Your version: 0.6.0 Latest version: 0.7.0
# Generated by Neurodocker version 0.6.0
# Timestamp: 2021-04-13 14:10:53 UTC
# Timestamp: 2021-06-07 18:59:26 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
Expand Down Expand Up @@ -44,6 +44,7 @@ ENTRYPOINT ["/neurodocker/startup.sh"]
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
fsl-core \
fsl-mni152-templates \
git \
num-utils \
gcc \
Expand Down Expand Up @@ -116,4 +117,122 @@ ENV IS_DOCKER="1"

WORKDIR /tmp/

ENTRYPOINT ["/neurodocker/startup.sh", "bidsonym"]
ENTRYPOINT ["/neurodocker/startup.sh", "bidsonym"]

RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "neurodebian:stretch-non-free" \
\n ], \
\n [ \
\n "install", \
\n [ \
\n "fsl-core", \
\n "fsl-mni152-templates", \
\n "git", \
\n "num-utils", \
\n "gcc", \
\n "g++", \
\n "curl", \
\n "build-essential", \
\n "nano" \
\n ] \
\n ], \
\n [ \
\n "run_bash", \
\n "curl -sL https://deb.nodesource.com/setup_10.x | bash - && apt-get install -y nodejs && apt-get install -y npm" \
\n ], \
\n [ \
\n "add_to_entrypoint", \
\n "source /etc/fsl/fsl.sh" \
\n ], \
\n [ \
\n "miniconda", \
\n { \
\n "conda_install": [ \
\n "python=3.6", \
\n "numpy", \
\n "nipype", \
\n "nibabel", \
\n "pandas" \
\n ], \
\n "pip_install": [ \
\n "deepdefacer", \
\n "tensorflow", \
\n "scikit-image" \
\n ], \
\n "create_env": "bidsonym", \
\n "activate": true \
\n } \
\n ], \
\n [ \
\n "run_bash", \
\n "source activate bidsonym && git clone https://github.com/poldracklab/pydeface.git && cd pydeface && python setup.py install && cd -" \
\n ], \
\n [ \
\n "run_bash", \
\n "source activate bidsonym && git clone https://github.com/nipy/quickshear.git && cd quickshear && python setup.py install && cd -" \
\n ], \
\n [ \
\n "run_bash", \
\n "source activate bidsonym && git clone https://github.com/neuronets/nobrainer.git && cd nobrainer && python setup.py install && cd -" \
\n ], \
\n [ \
\n "run_bash", \
\n "mkdir -p /opt/nobrainer/models && cd /opt/nobrainer/models && curl -LJO https://github.com/neuronets/nobrainer-models/releases/download/0.1/brain-extraction-unet-128iso-model.h5 && cd ~ " \
\n ], \
\n [ \
\n "run_bash", \
\n "git clone https://github.com/mih/mridefacer" \
\n ], \
\n [ \
\n "env", \
\n { \
\n "MRIDEFACER_DATA_DIR": "/mridefacer/data" \
\n } \
\n ], \
\n [ \
\n "run_bash", \
\n "npm install -g [email protected]" \
\n ], \
\n [ \
\n "run_bash", \
\n "mkdir /home/mri-deface-detector && cd /home/mri-deface-detector && npm install sharp --unsafe-perm && npm install -g mri-deface-detector --unsafe-perm && cd ~" \
\n ], \
\n [ \
\n "run_bash", \
\n "git clone https://github.com/miykael/gif_your_nifti && cd gif_your_nifti && source activate bidsonym && python setup.py install" \
\n ], \
\n [ \
\n "copy", \
\n [ \
\n ".", \
\n "/home/bm" \
\n ] \
\n ], \
\n [ \
\n "run_bash", \
\n "chmod a+x /home/bm/bidsonym/fs_data/mri_deface" \
\n ], \
\n [ \
\n "run_bash", \
\n "source activate bidsonym && cd /home/bm && pip install -e ." \
\n ], \
\n [ \
\n "env", \
\n { \
\n "IS_DOCKER": "1" \
\n } \
\n ], \
\n [ \
\n "workdir", \
\n "/tmp/" \
\n ], \
\n [ \
\n "entrypoint", \
\n "/neurodocker/startup.sh bidsonym" \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
21 changes: 7 additions & 14 deletions bidsonym/defacing_algorithms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ def run_quickshear(image, outfile):
deface_wf.run()


def mridefacer_cmd(image, subject_label, bids_dir):
def mridefacer_cmd(image, T1_file):
"""
Setup mridefacer command.
Expand All @@ -146,20 +146,14 @@ def mridefacer_cmd(image, subject_label, bids_dir):
import os
from shutil import move

cmd = ["/mridefacer/mridefacer", "--apply", image]
outdir = T1_file[:T1_file.rfind('/')]

cmd = ["/mridefacer/mridefacer", "--apply", image, "--outdir", outdir]
check_call(cmd)
path = os.path.join(bids_dir, "sourcedata/bidsonym/sub-%s" % subject_label)
facemask = os.path.join(bids_dir, "sub-%s" % subject_label,
"anat/sub-%s_T1w_defacemask.nii.gz" % subject_label)
if os.path.isdir(path) is True:
move(facemask, os.path.join(path))
else:
os.makedirs(path)
move(facemask, os.path.join(path))
return


def run_mridefacer(image, subject_label, bids_dir):
def run_mridefacer(image, T1_file):
"""
Setup and mridefacer workflow.
Expand All @@ -176,14 +170,13 @@ def run_mridefacer(image, subject_label, bids_dir):
deface_wf = pe.Workflow('deface_wf')
inputnode = pe.Node(niu.IdentityInterface(['in_file']),
name='inputnode')
mridefacer = pe.Node(Function(input_names=['image', 'subject_label', 'bids_dir'],
mridefacer = pe.Node(Function(input_names=['image', 'T1_file'],
output_names=['outfile'],
function=mridefacer_cmd),
name='mridefacer')
deface_wf.connect([(inputnode, mridefacer, [('in_file', 'image')])])
inputnode.inputs.in_file = image
mridefacer.inputs.subject_label = subject_label
mridefacer.inputs.bids_dir = bids_dir
mridefacer.inputs.T1_file = T1_file
deface_wf.run()


Expand Down
4 changes: 2 additions & 2 deletions bidsonym/run_deeid.py
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ def run_deeid():

if args.brainextraction is None:
raise Exception("For post defacing quality it is required to run a form of brainextraction"
"on the non-deindentified data. Thus please either indicate bet"
"on the non-deindentified data. Thus please either indicate bet "
"(--brainextration bet) or nobrainer (--brainextraction nobrainer).")

if args.skip_bids_validation:
Expand Down Expand Up @@ -146,7 +146,7 @@ def run_deeid():
elif args.deid == "quickshear":
run_quickshear(source_t1w, T1_file)
elif args.deid == "mridefacer":
run_mridefacer(source_t1w, subject_label, args.bids_dir)
run_mridefacer(source_t1w, T1_file)
elif args.deid == "deepdefacer":
run_deepdefacer(source_t1w, subject_label, args.bids_dir)

Expand Down
2 changes: 1 addition & 1 deletion generate_images.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ generate_docker() {
docker run --rm kaczmarj/neurodocker:0.6.0 generate docker \
--base neurodebian:stretch-non-free \
--pkg-manager apt \
--install fsl-core git num-utils gcc g++ curl build-essential nano\
--install fsl-core fsl-mni152-templates git num-utils gcc g++ curl build-essential nano\
--run-bash "curl -sL https://deb.nodesource.com/setup_10.x | bash - && apt-get install -y nodejs && apt-get install -y npm"\
--add-to-entrypoint "source /etc/fsl/fsl.sh" \
--miniconda \
Expand Down

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