Latest developments 2023

README.md

@@ -1,3 +1,9 @@
+
+[![GitHub release (latest by date)](https://img.shields.io/github/v/release/scilus/extractor_flow)](https://github.com/scilus/extractor_flow/releases)
+[![Documentation Status](https://readthedocs.org/projects/extractor_flow/badge/?version=latest)](https://extractor_flow.readthedocs.io/en/latest/?badge=latest)
+[![Docker container badge](https://img.shields.io/docker/v/scilus/scilus-flows?label=docker&logo=docker&logoColor=white)](https://hub.docker.com/r/scilus/scilus-flows)
+
+
 ExtractorFlow pipeline
 ======================
 

USAGE

@@ -29,17 +29,17 @@ OPTIONAL ARGUMENTS (current value)
 
     --run_bet                           Run bet if your t1s are not brain extracted ($run_bet).
     --orig                              Extract all trk in diffusion space (if t1 has been provided) ($orig).
-    --extended                          Extract bundles ($extended).
     --keep_intermediate_steps           Keep intermediate steps ($keep_intermediate_steps). MUST be used if you need to debug.
 
     --quick_registration                If set, will choose antsRegistrationSyNQuick.sh instead of antsRegistrationSyN.sh ($quick_registration).
 
     --processes_bet_register_t1         Number of processes for T1 brain extraction task ($processes_bet_register_t1).
-    --processes_apply_registration      Number of processes for registration application ($processes_apply_registration).
+    --processes_major_filtering         Number of processes for the major filtering task ($processes_major_filtering).
     --processes                         The number of parallel processes to launch ($cpu_count).
                                         Only affects the local scheduler.
 
-AVAILABLE PROFILES (using -profile option (e.g. -profile macos))
+AVAILABLE PROFILES (using -profile option (e.g. -profile macos,extract_bundles))
 
 macos                                   When this profile is used, ExtractorFlow will modify a parameter (scratch) for MacOS users.
 fully_reproducible                      When this profile is used, all the parameters will be set to have 100% reproducible results.
+extract_bundles                         Extract bundles

containers/Dockerfile

@@ -1,6 +1,7 @@
-FROM scilus/scilus:1.3.0
+FROM scilus/scilus:1.6.0
 
 WORKDIR /
 
-ADD JHU_template_GIN_dil.tar.bz2 /JHU_template_GIN_dil
-ADD filtering_lists.tar.bz2 /filtering_lists
+RUN mkdir extractor_flow
+ADD templates_and_ROIs.tar.bz2 /extractor_flow/
+ADD filtering_lists.tar.bz2 /extractor_flow/

containers/singularity_extractorflow.def

@@ -1,11 +1,11 @@
 BootStrap: docker
-From: scilus/scilus:1.3.0
+From: scilus/scilus:1.6.0
 
 %setup
-	export ROIs=JHU_template_GIN_dil.tar.bz2
-	mkdir $SINGULARITY_ROOTFS/JHU_template_GIN_dil
-	tar -jxf $ROIs -C $SINGULARITY_ROOTFS/JHU_template_GIN_dil
+	export ROIs=templates_and_ROIs.tar.bz2
+	mkdir -p $SINGULARITY_ROOTFS/extractor_flow/templates_and_ROIs
+	tar -jxf $ROIs -C $SINGULARITY_ROOTFS/extractor_flow/
 
 	export filtering_lists=filtering_lists.tar.bz2
-	mkdir $SINGULARITY_ROOTFS/filtering_lists
-	tar -jxf $filtering_lists -C $SINGULARITY_ROOTFS/filtering_lists
+	mkdir -p $SINGULARITY_ROOTFS/extractor_flow/filtering_lists
+	tar -jxf $filtering_lists -C $SINGULARITY_ROOTFS/extractor_flow/