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Update to use labelmerge v0.4.3 #50

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merged 8 commits into from
Feb 15, 2023
Merged

Update to use labelmerge v0.4.3 #50

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e605ea2
update scattr container version on release
kaitj Feb 15, 2023
b336de2
update to use labelmerge v0.4.3
kaitj Feb 15, 2023
bc38e1e
Remove fsl stage and related vars from Dockerfile
kaitj Feb 15, 2023
027d7fe
update path to ZonaBB dseg in config
kaitj Feb 15, 2023
f23a4f7
update template file names
kaitj Feb 15, 2023
bca029d
fix find for scattr container
kaitj Feb 15, 2023
a496af7
Remove unneeded comment in dockerfile
kaitj Feb 15, 2023
45bf053
Change spaces to tab in ZonaBB TSV
tkkuehn Feb 15, 2023
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7 changes: 7 additions & 0 deletions .github/workflows/release.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,13 @@ jobs:
find: version = "(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"
replace: version = "${{ env.NEW_RELEASE }}"

- name: Update container version
uses: jacobtomlinson/gha-find-replace@master
with:
include: scattr/config/snakebids.yml
find: 'scattr: "docker://khanlab/scattr:v(?:([0-9]+\.[0-9]+\.[0-9]+.+)|([0-9]+\.[0-9]+\.[0-9]+))"'
replace: 'scattr: "docker://khanlab/scattr:v${{ env.NEW_RELEASE }}"'

- name: Commit updates
env:
LATEST_VERSION: ${{ env.NEW_RELEASE }}
Expand Down
17 changes: 3 additions & 14 deletions Dockerfile
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Expand Up @@ -52,13 +52,6 @@ RUN wget https://github.com/ANTsX/ANTs/releases/download/v${ANTS_VER}/ants-${ANT
&& mv /opt/ants-${ANTS_VER} /opt/ants \
&& rm ants.zip

# Stage: FSL
# Copy over fslmaths to "minify"
FROM requirements as fsl
RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py \
&& python fslinstaller.py -d /opt/fsl \
&& rm fslinstaller.py

# Stage: build
FROM requirements AS build
COPY . /opt/scattr/
Expand All @@ -69,7 +62,7 @@ RUN cd /opt/scattr \

# Stage: runtime
# NOTE: use fsl stage for library dependencies
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FROM fsl AS runtime
FROM requirements AS runtime
COPY --from=mrtrix /opt/mrtrix3 /opt/mrtrix3
COPY --from=freesurfer /usr/local/freesurfer /usr/local/freesurfer
COPY --from=ants /opt/ants/bin/antsApplyTransforms /opt/ants/bin/antsRegistration /opt/ants/bin/antsRegistrationSyNQuick.sh /opt/ants/bin/
Expand All @@ -81,8 +74,8 @@ RUN WHEEL=`ls /opt/scattr | grep whl` \
&& apt-get --purge -y -qq autoremove
# Setup environments
ENV OS=Linux \
# Path: mrtrix > freesurfer > ants > fsl
PATH=/opt/mrtrix3/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/ants/:/opt/ants/bin:/opt/fsl/bin:$PATH \
# Path: mrtrix > freesurfer > ants
PATH=/opt/mrtrix3/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/ants/:/opt/ants/bin:$PATH \
# freesurfer specific
FREESURFER_HOME=/usr/local/freesurfer \
FREESURFER=/usr/local/freesurfer \
Expand All @@ -102,8 +95,4 @@ ENV OS=Linux \
PERL5LIB=/usr/local/freesurfer/mni/share/perl5 \
# ants specific
ANTSPATH=/opt/ants/bin/ \
# fsl specific
FSLDIR=/opt/fsl \
LD_LIBRARY_PATH=/opt/fsl/lib:$LD_LIBRARY_PATH \
FSLOUTPUTTYPE=NIFTI_GZ
ENTRYPOINT ["scattr"]
6 changes: 3 additions & 3 deletions scattr/config/snakebids.yml
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Expand Up @@ -171,14 +171,14 @@ parse_args:
Space: MNI152NLin6Asym

zona_bb_subcortex:
tsv: 'resources/zona_bb_subcortex/desc-ZonaBBSubcor_dseg.tsv'
tsv: 'resources/zona_bb_subcortex/desc-ZonaBB_dseg.tsv'
MNI152NLin6Asym:
dir: 'resources/zona_bb_subcortex/MNI152NLin6Asym/'
T1w: 'tpl-MNI152NLin6Asym_res-04_desc-brain_T1w.nii.gz'
seg: 'sub-SNSX32NLin2020Asym_space-MNI152NLin6Asym_desc-ZonaBBSubcor_dseg.nii.gz'
seg: 'sub-SNSX32NLin2020Asym_space-MNI152NLin6Asym_desc-ZonaBB_dseg.nii.gz'
MNI152NLin2009bAsym:
dir: 'resources/zona_bb_subcortex/MNI152NLin2009bAsym/'
seg: 'sub-SNSX32NLin2020Asym_space-MNI152NLin2009bAsym_desc-ZonaBBSubcor_dseg.nii.gz'
seg: 'sub-SNSX32NLin2020Asym_space-MNI152NLin2009bAsym_desc-ZonaBB_dseg.nii.gz'

# NOTE: This may not be needed with labelmerge
freesurfer:
Expand Down
0 ...in2009bAsym_desc-ZonaBBSubcor_dseg.nii.gz → ...I152NLin2009bAsym_desc-ZonaBB_dseg.nii.gz
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0 ...52NLin6Asym_desc-ZonaBBSubcor_dseg.nii.gz → ...e-MNI152NLin6Asym_desc-ZonaBB_dseg.nii.gz
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18 changes: 10 additions & 8 deletions ...a_bb_subcortex/desc-ZonaBBSubcor_dseg.tsv → ...es/zona_bb_subcortex/desc-ZonaBB_dseg.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,13 @@ index name
12 Right GPe
13 Left GPi
14 Right GPi
15 Left Hippocampus
16 Right Hippocampus
17 Left NAc
18 Right NAc
19 Left Amygdala
20 Right Amygdala
21 Left ZI
22 Right ZI
15 Left Thalamus
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I think 15 and 16 here should be separated by tabs and aren't

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Ahh, consequence of vscode. Will fix this.

16 Right Thalamus
17 Left Hippocampus
18 Right Hippocampus
19 Left NAc
20 Right NAc
21 Left Amygdala
22 Right Amygdala
23 Left ZI
24 Right ZI
55 changes: 4 additions & 51 deletions scattr/workflow/rules/zona_bb_subcortex.smk
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Expand Up @@ -34,7 +34,7 @@ rule cp_zona_tsv:
/ Path(config["zona_bb_subcortex"]["tsv"])
),
output:
zona_tsv=f"{zona_dir}/desc-ZonaBBSubcor_dseg.tsv",
zona_tsv=f"{zona_dir}/desc-ZonaBB_dseg.tsv",
threads: 1
resources:
mem_mb=4000,
Expand Down Expand Up @@ -121,57 +121,10 @@ rule warp2native:
"-o {output.nii} &> {log}"


rule rm_bb_thal:
"""Removes thalamus from existing parcellation

1. Grab labels following thalamus ROI
2. Remove existing thalamus from segmentation
3. Add labels following thalamus ROI back to segmentation
"""
input:
seg=rules.warp2native.output.nii,
output:
seg=bids_anat(
space="T1w",
desc="ZonaBBSubcor",
suffix="dseg.nii.gz",
),
non_thal=temp(
bids_anat(
space="T1w",
desc="NonThal",
suffix="dseg.nii.gz",
)
),
rm_seg=temp(
bids_anat(
space="T1w",
desc="ThalPost",
suffix="dseg.nii.gz",
)
),
threads: 4
resources:
mem_mb=16000,
time=10,
log:
f"{config['output_dir']}/logs/zona_bb_subcortex/sub-{{subject}}/rm_bb_thal.log",
group:
"subcortical_1"
container:
config["singularity"]["neuroglia-core"]
shell:
"fslmaths {input.seg} -sub 2 {output.non_thal} &> {log} && "
"fslmaths {output.non_thal} -thr 15 {output.non_thal} >> {log} 2>&1 && "
"fslmaths {input.seg} -thr 15 {output.rm_seg} >> {log} 2>&1 && "
"fslmaths {input.seg} -sub {output.rm_seg} {output.seg} >> {log} 2>&1 && "
"fslmaths {output.seg} -add {output.non_thal} {output.seg} >> {log} 2>&1"


rule labelmerge:
input:
zona_seg=expand(
rules.rm_bb_thal.output.seg,
rules.warp2native.output.nii,
subject=config["input_lists"]["T1w"]["subject"],
allow_missing=True,
),
Expand All @@ -185,7 +138,7 @@ rule labelmerge:
params:
zona_dir=zona_dir,
fs_dir=rules.thalamic_segmentation.input.freesurfer_dir,
zona_desc="ZonaBBSubcor",
zona_desc="ZonaBB",
fs_desc="FreesurferThal",
labelmerge_dir=directory(labelmerge_dir),
output:
Expand Down Expand Up @@ -218,7 +171,7 @@ rule labelmerge:
container:
config["singularity"]["labelmerge"]
shell:
"labelmerge {params.zona_dir} {params.labelmerge_dir} participant --base_desc {params.zona_desc} --overlay_bids_dir {params.fs_dir} --overlay_desc {params.fs_desc} --cores {threads} --force-output"
"labelmerge {params.zona_dir} {params.labelmerge_dir} participant --base_desc {params.zona_desc} --overlay_bids_dir {params.fs_dir} --overlay_desc {params.fs_desc} --base_drop 15 16 --cores {threads} --force-output"


rule get_num_nodes:
Expand Down