From bcbd76acec97c2fb6b226aaac51ab0458a0af285 Mon Sep 17 00:00:00 2001 From: Arshitha Basavaraj Date: Mon, 24 Apr 2023 10:56:22 -0400 Subject: [PATCH] Update README.md --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 58e7a21..a7345fe 100644 --- a/README.md +++ b/README.md @@ -84,7 +84,7 @@ placeholders for paths to input and output directories, respectively. If you have a small dataset with less than 10 subjects, then it might be easiest to run the defacing algorithm serially. ```bash -python dsst_defacing_wf.py -i ${INPUT_DIR} -o ${OUTPUT_DIR} +python dsst-defacing-pipeline/src/dsst_defacing_wf.py -i ${INPUT_DIR} -o ${OUTPUT_DIR} ``` #### Option 2: In parallel at subject level @@ -102,7 +102,7 @@ a. Assuming these scripts are run on the NIH HPC system, the first step would be for i in `ls -d ${INPUT_DIR}/sub-*`; do \ SUBJ=$(echo $i | sed "s|${INPUT_DIR}/||g" ); \ - echo "python src/dsst_defacing_wf.py -i ${INPUT_DIR} -o ${OUTPUT_DIR} -p ${SUBJ}"; \ + echo "python dsst-defacing-pipeline/src/dsst_defacing_wf.py -i ${INPUT_DIR} -o ${OUTPUT_DIR} -p ${SUBJ}"; \ done > defacing_parallel_subject_level.swarm ``` @@ -126,7 +126,7 @@ for i in `ls -d ${INPUT_DIR}/sub-*`; do SUBJ=$(echo $i | sed "s|${INPUT_DIR}/||g" ); for j in `ls -d ${INPUT_DIR}/${SUBJ}/ses-*`; do SESS=$(echo $j | sed "s|${INPUT_DIR}/${SUBJ}/||g" ) - echo "python src/dsst_defacing_wf.py -i ${INPUT_DIR} -o ${OUTPUT_DIR} -p ${SUBJ} -s ${SESS}"; + echo "python dsst-defacing-pipeline/src/dsst_defacing_wf.py -i ${INPUT_DIR} -o ${OUTPUT_DIR} -p ${SUBJ} -s ${SESS}"; done; done > defacing_parallel_session_level.swarm ``` @@ -140,7 +140,7 @@ swarm -f defacing_parallel_session_level.swarm --merge-output --logdir ${OUTPUT_ Generate 3D renders for every defaced image in the output directory. ```bash - python src/generate_renders.py -o ${OUTPUT_DIR} + python dsst-defacing-pipeline/src/generate_renders.py -o ${OUTPUT_DIR} ``` ### Visual Inspection