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[BUG] Fix fs_stats 0.2.2 and set the version to 0.3.0 #68

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Merged
michellewang merged 9 commits into from
Oct 29, 2026
Merged

[BUG] Fix fs_stats 0.2.2 and set the version to 0.3.0 #68

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e7d96e1
treat as separate version and add to test config
michellewang Oct 28, 2026
f966a2f
Merge remote-tracking branch 'upstream/main' into fs_stats_docker
michellewang Oct 28, 2026
19f51eb
revert to apptainer/singularity being the default and docker being th…
michellewang Oct 28, 2026
f208ab0
fix conftest
michellewang Oct 28, 2026
2bafd86
fix pipeline not working with nipoppy 0.4.8
michellewang Oct 28, 2026
667ac66
remove container command arg
michellewang Oct 28, 2026
6e4e485
Merge remote-tracking branch 'upstream/main' into fs_stats_docker
michellewang Oct 29, 2026
dba5e65
fix failing test
michellewang Oct 29, 2026
b26d81b
bumpt version to 0.3.0
michellewang Oct 29, 2026
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24 changes: 0 additions & 24 deletions pipelines/extraction/fs_stats-0.2.2/invocation-docker.json
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1 change: 0 additions & 1 deletion pipelines/extraction/fs_stats-0.2.2/requirements.txt
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12 changes: 3 additions & 9 deletions ...nes/extraction/fs_stats-0.2.2/config.json → ...nes/extraction/fs_stats-0.3.0/config.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"NAME": "fs_stats",
"VERSION": "0.2.2",
"VERSION": "0.3.0",
"CONTAINER_INFO": {
"FILE": "[[NIPOPPY_DPATH_CONTAINERS]]/freesurfer_7.3.2.sif",
"URI": "docker://freesurfer/freesurfer:7.3.2"
Expand All @@ -10,7 +10,8 @@
"FS_LICENSE": "[[FREESURFER_LICENSE_FILE]]"
},
"BIND_PATHS": [
"[[FREESURFER_LICENSE_FILE]]"
"[[FREESURFER_LICENSE_FILE]]",
"[[NIPOPPY_DPATH_PIPELINES]]"
]
},
"PROC_DEPENDENCIES": [
Expand All @@ -25,13 +26,6 @@
"DESCRIPTOR_FILE": "descriptor.json",
"HPC_CONFIG_FILE": "hpc.json",
"ANALYSIS_LEVEL": "group"
},
{
"NAME": "docker",
"INVOCATION_FILE": "invocation-docker.json",
"DESCRIPTOR_FILE": "descriptor.json",
"HPC_CONFIG_FILE": "hpc.json",
"ANALYSIS_LEVEL": "group"
}
],
"VARIABLES": {
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13 changes: 2 additions & 11 deletions ...extraction/fs_stats-0.2.2/descriptor.json → ...extraction/fs_stats-0.3.0/descriptor.json
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
{
"name": "fs_stats",
"description": "FreeSurfer aseg/aparc stats (and QC metrics) extractor",
"tool-version": "0.2.2",
"tool-version": "0.3.0",
"schema-version": "0.5",
"command-line": "python [SCRIPT_PATH] [INPUT_DIR_PATH] [OUTPUT_DIR_PATH] [MODE] [WITH_QC] [ASEG_MEASURES] [APARC_PARCELLATIONS] [APARC_MEASURES] [CONTAINER] [ASEG_ARGS] [APARC_ARGS] [EULER_SURF_PATHS] [CNR_VOL_PATHS] [CNR_MEASURES] [SUB_COLNAME] [SES_COLNAME] [SUB_PREFIX] [SES_PREFIX] [VERBOSE]",
"command-line": "fspython [SCRIPT_PATH] [INPUT_DIR_PATH] [OUTPUT_DIR_PATH] [MODE] [WITH_QC] [ASEG_MEASURES] [APARC_PARCELLATIONS] [APARC_MEASURES] [ASEG_ARGS] [APARC_ARGS] [EULER_SURF_PATHS] [CNR_VOL_PATHS] [CNR_MEASURES] [SUB_COLNAME] [SES_COLNAME] [SUB_PREFIX] [SES_PREFIX] [VERBOSE]",
"inputs": [
{
"name": "script_path",
Expand Down Expand Up @@ -81,15 +81,6 @@
"command-line-flag": "--aparc-measures",
"value-key": "[APARC_MEASURES]"
},
{
"name": "container",
"id": "container",
"description": "Container command and arguments (including image file), as a single string. This needs to contain everything needed to be able to run the FreeSurfer commands, for example \"apptainer exec --bind <INPUT_DIR_PATH> <IMAGE_FILE_PATH>\". Does not need to be specified if running on a system with FreeSurfer installed. IMPORTANT: only the Singularity/Apptainer container engine is explicitly supported because it allows for forwarding environment variables; this script might work with Docker containers but likely only with --mode single.",
"type": "String",
"optional": true,
"command-line-flag": "--container",
"value-key": "[CONTAINER]"
},
{
"name": "aseg_args",
"id": "aseg_args",
Expand Down
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