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Fix path and acq and rec search
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@Shotgunosine
Shotgunosine committed Jun 29, 2020
1 parent 6d40956 commit c52c7f0
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12 changes: 3 additions & 9 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Generated by Neurodocker version 0.4.2-3-gf7055a1
# Timestamp: 2020-06-26 19:59:46 UTC
# Timestamp: 2020-06-29 16:04:34 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 @@ -131,8 +131,6 @@ ENV FSLDIR="/usr/share/fsl/5.0" \
FSLTCLSH="/usr/bin/tclsh" \
FSLWISH="/usr/bin/wish"

RUN bash -c 'PATH=/usr/lib/fsl/5.0:$PATH'

ENV OS="Linux" \
FS_OVERRIDE="0" \
FIX_VERTEX_AREA="" \
Expand All @@ -148,7 +146,7 @@ ENV OS="Linux" \
FMRI_ANALYSIS_DIR="/opt/freesurfer/fsfast" \
PERL5LIB="/opt/freesurfer/mni/share/perl5" \
MNI_PERL5LIB="/opt/freesurfer/mni/share/perl5/" \
PATH="/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \
PATH="/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \
PYTHONPATH=""

RUN mkdir root/matlab && touch root/matlab/startup.m
Expand Down Expand Up @@ -239,10 +237,6 @@ RUN echo '{ \
\n } \
\n ], \
\n [ \
\n "run_bash", \
\n "PATH=/usr/lib/fsl/5.0:$PATH" \
\n ], \
\n [ \
\n "env", \
\n { \
\n "OS": "Linux", \
Expand All @@ -260,7 +254,7 @@ RUN echo '{ \
\n "FMRI_ANALYSIS_DIR": "/opt/freesurfer/fsfast", \
\n "PERL5LIB": "/opt/freesurfer/mni/share/perl5", \
\n "MNI_PERL5LIB": "/opt/freesurfer/mni/share/perl5/", \
\n "PATH": "/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", \
\n "PATH": "/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", \
\n "PYTHONPATH": "" \
\n } \
\n ], \
Expand Down
65 changes: 43 additions & 22 deletions Singularity
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Generated by Neurodocker version 0.4.2-3-gf7055a1
# Timestamp: 2020-06-26 19:59:47 UTC
# Timestamp: 2020-06-29 16:04:35 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
Expand Down Expand Up @@ -43,11 +43,6 @@ apt-get install -y -q --no-install-recommends \
perl-modules \
wget \
curl \
python3 \
python3-pip \
python3-pandas \
python-pip \
python3-setuptools \
libsm-dev \
libx11-dev \
libxt-dev \
Expand Down Expand Up @@ -85,7 +80,30 @@ curl -fsSL --retry 5 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/
--exclude='freesurfer/trctrain'
sed -i '$isource "/opt/freesurfer/SetUpFreeSurfer.sh"' "$ND_ENTRYPOINT"

bash -c 'pip3 install nibabel pandas==0.21.0'
export PATH="/opt/miniconda-latest/bin:$PATH"
echo "Downloading Miniconda installer ..."
conda_installer="/tmp/miniconda.sh"
curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash "$conda_installer" -b -p /opt/miniconda-latest
rm -f "$conda_installer"
conda update -yq -nbase conda
conda config --system --prepend channels conda-forge
conda config --system --set auto_update_conda false
conda config --system --set show_channel_urls true
sync && conda clean -tipsy && sync
conda install -y -q --name base \
'python=3' \
'pip' \
'pandas' \
'setuptools' \
'pandas=0.21.0'
sync && conda clean -tipsy && sync
bash -c "source activate base
pip install --no-cache-dir \
'nibabel'"
rm -rf ~/.cache/pip/*
sync


bash -c 'curl -sL https://deb.nodesource.com/setup_6.x | bash -'

Expand All @@ -97,8 +115,6 @@ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

bash -c 'npm install -g [email protected]'

bash -c 'PATH=/usr/lib/fsl/5.0:$PATH'

mkdir root/matlab && touch root/matlab/startup.m

mkdir /scratch
Expand Down Expand Up @@ -131,11 +147,6 @@ echo '{
\n "perl-modules",
\n "wget",
\n "curl",
\n "python3",
\n "python3-pip",
\n "python3-pandas",
\n "python-pip",
\n "python3-setuptools",
\n "libsm-dev",
\n "libx11-dev",
\n "libxt-dev",
Expand All @@ -151,8 +162,20 @@ echo '{
\n }
\n ],
\n [
\n "run_bash",
\n "pip3 install nibabel pandas==0.21.0"
\n "miniconda",
\n {
\n "use_env": "base",
\n "conda_install": [
\n "python=3",
\n "pip",
\n "pandas",
\n "setuptools",
\n "pandas=0.21.0"
\n ],
\n "pip_install": [
\n "nibabel"
\n ]
\n }
\n ],
\n [
\n "run_bash",
Expand Down Expand Up @@ -181,10 +204,6 @@ echo '{
\n }
\n ],
\n [
\n "run_bash",
\n "PATH=/usr/lib/fsl/5.0:$PATH"
\n ],
\n [
\n "env",
\n {
\n "OS": "Linux",
Expand All @@ -202,7 +221,7 @@ echo '{
\n "FMRI_ANALYSIS_DIR": "/opt/freesurfer/fsfast",
\n "PERL5LIB": "/opt/freesurfer/mni/share/perl5",
\n "MNI_PERL5LIB": "/opt/freesurfer/mni/share/perl5/",
\n "PATH": "/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
\n "PATH": "/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
\n "PYTHONPATH": ""
\n }
\n ],
Expand Down Expand Up @@ -249,6 +268,8 @@ export LC_ALL="en_US.UTF-8"
export ND_ENTRYPOINT="/neurodocker/startup.sh"
export FREESURFER_HOME="/opt/freesurfer"
export PATH="/opt/freesurfer/bin:$PATH"
export CONDA_DIR="/opt/miniconda-latest"
export PATH="/opt/miniconda-latest/bin:$PATH"
export FSLDIR="/usr/share/fsl/5.0"
export FSLOUTPUTTYPE="NIFTI_GZ"
export FSLMULTIFILEQUIT="TRUE"
Expand All @@ -271,7 +292,7 @@ export MNI_DATAPATH="/opt/freesurfer/mni/data"
export FMRI_ANALYSIS_DIR="/opt/freesurfer/fsfast"
export PERL5LIB="/opt/freesurfer/mni/share/perl5"
export MNI_PERL5LIB="/opt/freesurfer/mni/share/perl5/"
export PATH="/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
export PATH="/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
export PYTHONPATH=""

%files
Expand Down
6 changes: 2 additions & 4 deletions generate_freesurfer_images.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,14 +55,13 @@ docker run --rm ${image} generate docker \
--env FSLDIR=/usr/share/fsl/5.0 FSLOUTPUTTYPE=NIFTI_GZ \
FSLMULTIFILEQUIT=TRUE POSSUMDIR=/usr/share/fsl/5.0 LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
FSLTCLSH=/usr/bin/tclsh FSLWISH=/usr/bin/wish FSLOUTPUTTYPE=NIFTI_GZ \
--run-bash 'PATH=/usr/lib/fsl/5.0:$PATH' \
--env OS=Linux FS_OVERRIDE=0 FIX_VERTEX_AREA= SUBJECTS_DIR=/opt/freesurfer/subjects \
FSF_OUTPUT_FORMAT=nii.gz MNI_DIR=/opt/freesurfer/mni LOCAL_DIR=/opt/freesurfer/local \
FREESURFER_HOME=/opt/freesurfer FSFAST_HOME=/opt/freesurfer/fsfast MINC_BIN_DIR=/opt/freesurfer/mni/bin \
MINC_LIB_DIR=/opt/freesurfer/mni/lib MNI_DATAPATH=/opt/freesurfer/mni/data \
FMRI_ANALYSIS_DIR=/opt/freesurfer/fsfast PERL5LIB=/opt/freesurfer/mni/share/perl5 \
MNI_PERL5LIB=/opt/freesurfer/mni/share/perl5/ \
PATH=/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
PATH=/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
PYTHONPATH="" \
--run 'mkdir root/matlab && touch root/matlab/startup.m' \
--run 'mkdir /scratch' \
Expand All @@ -88,14 +87,13 @@ docker run --rm ${image} generate singularity \
--env FSLDIR=/usr/share/fsl/5.0 FSLOUTPUTTYPE=NIFTI_GZ \
FSLMULTIFILEQUIT=TRUE POSSUMDIR=/usr/share/fsl/5.0 LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
FSLTCLSH=/usr/bin/tclsh FSLWISH=/usr/bin/wish FSLOUTPUTTYPE=NIFTI_GZ \
--run-bash 'PATH=/usr/lib/fsl/5.0:$PATH' \
--env OS=Linux FS_OVERRIDE=0 FIX_VERTEX_AREA= SUBJECTS_DIR=/opt/freesurfer/subjects \
FSF_OUTPUT_FORMAT=nii.gz MNI_DIR=/opt/freesurfer/mni LOCAL_DIR=/opt/freesurfer/local \
FREESURFER_HOME=/opt/freesurfer FSFAST_HOME=/opt/freesurfer/fsfast MINC_BIN_DIR=/opt/freesurfer/mni/bin \
MINC_LIB_DIR=/opt/freesurfer/mni/lib MNI_DATAPATH=/opt/freesurfer/mni/data \
FMRI_ANALYSIS_DIR=/opt/freesurfer/fsfast PERL5LIB=/opt/freesurfer/mni/share/perl5 \
MNI_PERL5LIB=/opt/freesurfer/mni/share/perl5/ \
PATH=/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
PATH=/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
PYTHONPATH="" \
--run 'mkdir root/matlab && touch root/matlab/startup.m' \
--run 'mkdir /scratch' \
Expand Down
55 changes: 28 additions & 27 deletions run.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -127,15 +127,25 @@ def run(command, env={}, ignore_errors=False):

subject_dirs = glob(os.path.join(args.bids_dir, "sub-*"))

if args.acquisition_label:
acq_tpl = "*acq-%s*" % args.acquisition_label
#Got to combine acq_tpl and rec_tpl
if args.acquisition_label and not args.reconstruction_label:
ar_tpl = "*acq-%s*" % args.acquisition_label
elif args.reconstruction_label and not args.acquisition_label:
ar_tpl = "*rec-%s*" % args.reconstruction_label
elif args.reconstruction_label and args.acquisition_label:
ar_tpl = "*acq-%s*_rec-%s*" % (args.acquisition_label, args.reconstruction_label)
else:
acq_tpl = "*"

if args.reconstruction_label:
rec_tpl = "*rec-%s*" % args.reconstruction_label
ar_tpl = "*"

#Got to combine acq_tpl and rec_tpl
if args.refine_pial_acquisition_label and not args.refine_pial_reconstruction_label:
ar_t2 = "*acq-%s*" % args.refine_pial_acquisition_label
elif args.refine_pial_reconstruction_label and not args.refine_pial_acquisition_label:
ar_t2 = "*rec-%s*" % args.refine_pial_reconstruction_label
elif args.refine_pial_reconstruction_label and args.refine_pial_acquisition_label:
ar_t2 = "*acq-%s*_rec-%s*" % (args.refine_pial_acquisition_label, args.refine_pial_reconstruction_label)
else:
rec_tpl = "*"
ar_t2 = "*"

# if there are session folders, check if study is truly longitudinal by
# searching for the first subject with more than one valid sessions
Expand All @@ -150,7 +160,7 @@ def run(command, env={}, ignore_errors=False):
if glob(os.path.join(args.bids_dir, "sub-%s" % subject_label,
"ses-%s" % session_label,
"anat",
"%s_T1w.nii*" % acq_tpl)):
"%s_T1w.nii*" % ar_tpl)):
n_valid_sessions += 1
if n_valid_sessions > 1:
multi_session_study = True
Expand All @@ -161,15 +171,6 @@ def run(command, env={}, ignore_errors=False):
else:
longitudinal_study = False

if args.refine_pial_acquisition_label:
acq_t2 = "*acq-%s*" % args.refine_pial_acquisition_label
else:
acq_t2 = "*"

if args.refine_pial_reconstruction_label:
rec_t2 = "*rec-%s*" % args.refine_pial_reconstruction_label
else:
rec_t2 = "*"

subjects_to_analyze = []
# only for a subset of subjects
Expand Down Expand Up @@ -208,7 +209,7 @@ def run(command, env={}, ignore_errors=False):
"sub-%s" % subject_label,
"ses-*",
"anat",
"%s_%s_T1w.nii*" % (acq_tpl, rec_tpl)))
"%s_T1w.nii*" % (ar_tpl)))
sessions = set([os.path.normpath(t1).split(os.sep)[-3].split("-")[-1] for t1 in T1s])
if args.session_label:
sessions = sessions.intersection(args.session_label)
Expand All @@ -222,7 +223,7 @@ def run(command, env={}, ignore_errors=False):
"sub-%s" % subject_label,
"ses-%s" % session_label,
"anat",
"%s_%s_T1w.nii*" % (acq_tpl, rec_tpl)))
"%s_T1w.nii*" % (ar_tpl)))
input_args = ""

if three_T == 'true':
Expand All @@ -238,10 +239,10 @@ def run(command, env={}, ignore_errors=False):

T2s = glob(os.path.join(args.bids_dir, "sub-%s" % subject_label,
"ses-%s" % session_label, "anat",
"%s_%s_T2w.nii*" % (acq_t2, rec_t2)))
"%s_T2w.nii*" % (ar_t2)))
FLAIRs = glob(os.path.join(args.bids_dir, "sub-%s" % subject_label,
"ses-%s" % session_label, "anat",
"%s_%s_FLAIR.nii*" % (acq_t2, rec_t2)))
"%s_FLAIR.nii*" % (ar_t2)))
if args.refine_pial == "T2":
for T2 in T2s:
if (max(nibabel.load(T2).header.get_zooms()) < 1.2) | args.allow_lowresT2:
Expand Down Expand Up @@ -338,7 +339,7 @@ def run(command, env={}, ignore_errors=False):
"sub-%s" % subject_label,
"ses-*",
"anat",
"%s_%s_T1w.nii*" % (acq_tpl, rec_tpl)))
"%s_T1w.nii*" % (ar_tpl)))
input_args = ""

if three_T == 'true':
Expand All @@ -356,12 +357,12 @@ def run(command, env={}, ignore_errors=False):
"sub-%s" % subject_label,
"ses-*",
"anat",
"%s_%s_T2w.nii*" % (acq_t2, rec_t2)))
"%s_T2w.nii*" % (ar_t2)))
FLAIRs = glob(os.path.join(args.bids_dir,
"sub-%s" % subject_label,
"ses-*",
"anat",
"%s_%s_FLAIR.nii*" % (acq_t2, rec_t2)))
"%s_FLAIR.nii*" % (ar_t2)))
if args.refine_pial == "T2":
for T2 in T2s:
if (max(nibabel.load(T2).header.get_zooms()) < 1.2) | args.allow_lowresT2:
Expand Down Expand Up @@ -408,7 +409,7 @@ def run(command, env={}, ignore_errors=False):
T1s = glob(os.path.join(args.bids_dir,
"sub-%s" % subject_label,
"anat",
"%s_%s_T1w.nii*" % (acq_tpl, rec_tpl)))
"%s_T1w.nii*" % (ar_tpl)))
if not T1s:
print("No T1w nii files found for subject %s. Skipping subject." % subject_label)
continue
Expand All @@ -426,9 +427,9 @@ def run(command, env={}, ignore_errors=False):
input_args += " -hires"
input_args += " -i %s" % T1
T2s = glob(os.path.join(args.bids_dir, "sub-%s" % subject_label, "anat",
"%s_%s_T2w.nii*" % (acq_t2, rec_t2)))
"%s_T2w.nii*" % (ar_t2)))
FLAIRs = glob(os.path.join(args.bids_dir, "sub-%s" % subject_label, "anat",
"%s_%s_FLAIR.nii*" % (acq_t2, rec_t2)))
"%s_FLAIR.nii*" % (ar_t2)))
if args.refine_pial == "T2":
for T2 in T2s:
if max(nibabel.load(T2).header.get_zooms()) < 1.2:
Expand Down

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