Fs longitudinal client scripts

examples/freesurfer/freesurfer-args.json

@@ -1,6 +1,6 @@
 {
-    "image": "/vip/Home/API/reconall-example/INPUTS/ds001600/sub-1/anat/sub-1_T1w.nii.gz",
-    "results-directory": "/vip/Home/API/reconall-example/OUTPUTS/",
-    "options": "-all",
-    "license key": "/vip/Home/API/reconall-example/INPUTS/LICENSE.txt"
-}
+    "nifti": "/vip/Home/API/reconall-example/INPUTS/ds001600/sub-1/anat/sub-1_T1w.nii.gz",
+    "subjid": "sub-1_T1w",
+    "directives": "-all",
+    "license": "/vip/Home/API/reconall-example/INPUTS/LICENSE.txt"
+}

examples/freesurfer/freesurfer-recon-all.sh

@@ -3,6 +3,6 @@
 python3 ./vip-cli.py \
     --session reconall-example \
     --input $(realpath ./inputs) \
-    --pipeline "Freesurfer (recon-all)/0.3.8" \
+    --pipeline "Freesurfer-Recon-all/7.3.1" \
     --arguments freesurfer-args.json \
     --api-key VIP_API_TOKEN

examples/freesurfer/freesurfer_longitudinal_processing/1-girder_download_input_data.py

@@ -0,0 +1,46 @@
+# Description:
+# Author: Frederic Cervenansky < frederic.cervenansky@creatis.insa-lyon.fr>
+#
+# Licence Cecill-B
+# Copyright (C) Creatis 2017-2024
+
+
+# import
+import girder_client
+import types
+import sys
+import click
+from pathlib import Path
+
+# api Rest url of the warehouse
+#Windows users: paths use backslashes (\) while Linux/macOS use forward slashes (/)
+url='https://insert/your-server-here/api/v1'
+#example URLs would be:
+# https://srmnopt.creatis.insa-lyon.fr/warehouse/api/v1 --> for NMR and Optics
+# https://myriad.creatis.insa-lyon.fr/api/v1 --> for MYRIAD
+
+# apiKey is a "mechanism" to share authentication and rights on folder.
+# User should defined through the web interface (inside user information) an apiKey ith the corresponding privileges
+apiKey = 'GIRDER_API_KEY'
+
+# Generate the warehouse client
+gc = girder_client.GirderClient(apiUrl=url)
+
+# Authentication to the warehouse
+gc.authenticate(apiKey=apiKey)
+
+# Use the ID of the folder you chose put your input MRIs
+folderId ='FOLDER_ID' #  3D Flow phantom+Bubbles
+#an example of a folder ID: 698de7fe82d062f2aea9619d
+
+# Local download directory
+download_dir = Path('/insert/your/download/path')
+
+# Download data from Girder
+gc.downloadFolderRecursive(folderId, str(download_dir))
+
+# Add derivatives/freesurfer folder
+derivatives_fs = download_dir / 'derivatives' / 'freesurfer'
+derivatives_fs.mkdir(parents=True, exist_ok=True)  # will create if not exists, do nothing if exists
+
+print(f"'derivatives/freesurfer' folder ensured at: {derivatives_fs}")

examples/freesurfer/freesurfer_longitudinal_processing/2-FS_CROSS_parallel_jobs.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env -S uv run --script
+# /// script
+# requires-python = ">=3.11"
+# dependencies = [
+#     "vip-client",
+# ]
+
+from vip_client import VipSession
+from pathlib import Path
+import os 
+
+# This directory will be uploaded to VIP — ensure no sensitive data
+# (e.g., DICOMs, scripts containing API keys) is included. 
+input_dir = Path("/insert/your/input/path") # make sure license file is copied in this directory
+output_dir = Path("/insert/your/output/path/derivatives/freesurfer")
+
+# Save current working directory and change to /tmp (temporary workaround for VIP bug)
+orig_cwd = os.getcwd()  
+os.chdir('/tmp')    
+
+# Get T1w NIfTIs only from sub-* folders, excluding run-02, run-03, ...
+nifti_files = [
+    str(f)
+    for sub in input_dir.iterdir()
+    if sub.is_dir() and sub.name.startswith("sub-")
+    for f in sub.rglob("*.nii.gz")
+    if f.name.endswith("_T1w.nii.gz")
+    and ("_run-" not in f.name or "_run-01_" in f.name)
+]
+
+# Create subjid from filenames
+subjid = [Path(f).name.replace(".nii.gz", "") for f in nifti_files]
+
+input_settings = {
+    "nifti": nifti_files,
+    "license": str(input_dir / "license.txt"),
+    "subjid": subjid
+}
+
+session = VipSession.init(
+    api_key="VIP_API_KEY",
+    input_dir=str(input_dir),
+    output_dir= str(output_dir),
+    pipeline_id="FreeSurfer-Recon-all/7.3.1",
+    input_settings=input_settings
+)
+
+session.run_session()
+session.display()
+
+# Restore original working directory
+os.chdir(orig_cwd)
+
+# Download outputs to the output_dir
+session.download_outputs(get_status=['Finished', 'Killed'])
+
+# Optional cleanup of outputs on VIP 
+# session.finish()

examples/freesurfer/freesurfer_longitudinal_processing/3-tar_sub_TPs.py

@@ -0,0 +1,53 @@
+from pathlib import Path
+import tarfile
+import shutil
+
+fs_dir = Path("/insert/your/input/path/derivatives/freesurfer")
+tmp_dir = fs_dir / "tmp"
+
+# create a tmp directory if it doesn't exist
+tmp_dir.mkdir(exist_ok=True)
+
+# Collect eligible tarballs (.tar.gz or .tgz)
+tarballs = [
+    t for t in fs_dir.iterdir()
+    if t.is_file()
+    and t.suffixes in ([".tar", ".gz"], [".tgz"])
+    and "ses-" in t.name
+    and ".long." not in t.name
+]
+
+subjects = {}
+
+for tar_path in tarballs:
+    subj = tar_path.name.split("_")[0]  # sub-XXXX
+
+    # Remove full archive suffix safely
+    if tar_path.suffixes == [".tar", ".gz"]:
+        base_name = tar_path.name[:-7]   # remove ".tar.gz"
+    else:  # .tgz
+        base_name = tar_path.stem        # removes ".tgz"
+
+    extract_dir = tmp_dir / "extracted" / base_name
+    extract_dir.mkdir(parents=True, exist_ok=True)
+
+    # Untar (auto-detect compression)
+    with tarfile.open(tar_path, "r:*") as tar:
+        tar.extractall(path=extract_dir)
+
+    subjects.setdefault(subj, []).append(extract_dir)
+
+# Group per subject
+for subj, tp_dirs in subjects.items():
+    out_tar = tmp_dir / f"{subj}_TPs.tgz"
+
+    with tarfile.open(out_tar, "w:gz") as tar:
+        for tp_dir in tp_dirs:
+            for item in tp_dir.iterdir():
+                tar.add(item, arcname=item.name)
+
+# Cleanup extracted files
+shutil.rmtree(tmp_dir / "extracted", ignore_errors=True)
+
+print("✅ Done: grouped longitudinal timepoints per subject.")
+

examples/freesurfer/freesurfer_longitudinal_processing/4-FS_BASE_parallel_jobs.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env -S uv run --script
+# /// script
+# requires-python = ">=3.11"
+# dependencies = [
+#     "vip-client",
+# ]
+
+from vip_client import VipSession
+from pathlib import Path
+import os 
+
+# This directory will be uploaded to VIP — ensure no sensitive data
+# (e.g., DICOMs, scripts containing API keys) is included. 
+input_dir = Path("/insert/your/input/path/derivatives/freesurfer/tmp") #make sure license file is copied in this directory
+output_dir = Path("/insert/your/output/path/derivatives/freesurfer")
+
+# Save current working directory and change to /tmp (temporary workaround for VIP bug)
+orig_cwd = os.getcwd()  
+os.chdir('/tmp')      
+
+# Collect tarballs and BASE_IDs
+tp_tarballs = [f for f in input_dir.iterdir() if f.suffix in (".tgz", ".tar.gz") and "_TPs" in f.name]
+tp_tarballs.sort()  # optional
+
+base_ids = [f.name.split("_")[0] for f in tp_tarballs]
+
+# Build batch input settings
+input_settings = {
+    "LICENSE_FILE": str(input_dir / "license.txt"),
+    "TP_TARBALL": [str(f) for f in tp_tarballs],  # list of tarballs
+    "BASE_ID": base_ids,                           # list of base IDs
+}
+
+session = VipSession.init(
+    api_key="VIP_API_KEY",
+    input_dir=str(input_dir),
+    output_dir= str(output_dir),
+    pipeline_id="FreeSurfer-Recon-all-BASE/7.3.1",
+    input_settings=input_settings,
+)
+
+session.run_session()  # VIP will process tarballs in parallel
+session.display()
+
+# Restore original working directory
+os.chdir(orig_cwd)
+
+# Download outputs to the output_dir
+session.download_outputs(get_status=['Finished', 'Killed'])
+
+# Optional cleanup of outputs on VIP 
+# session.finish()
+
+# Delete tmp folder locally
+# WARNING: This removes the entire directory.
+# Make sure that the license file is stored in another safe location.
+shutil.rmtree(input_dir)
+print(f"Deleted temporary folder: {input_dir}")
+
+
+

examples/freesurfer/freesurfer_longitudinal_processing/5-FS_LONG_parallel_jobs.py

@@ -0,0 +1,82 @@
+#!/usr/bin/env python3
+# /// script
+# requires-python = ">=3.11"
+# dependencies = [
+#     "vip-client",
+# ]
+# ///
+
+from vip_client import VipSession
+from vip_client.utils import vip
+
+# VIP API Key
+API_KEY = "VIP_API_KEY"
+
+# Initialize VIP connection
+VipSession.init(api_key=API_KEY)
+
+# VIP paths 
+BASE_DIR = "/vip/Home/API/VipSession-xxxxxx-xxxxxx-bxx/OUTPUTS/YYYY-MM-DD_HHMMSS/" # from the output of BASE pipeline
+TP_DIR   = "/vip/Home/API/VipSession-xxxxxx-xxxxxx-bxx/INPUTS/" # from the input of BASE pipeline
+LICENSE_FILE = "/vip/Home/API/VipSession-xxxxxx-xxxxxx-bxx/INPUTS/license.txt" # from the input of BASE pipeline
+
+# Local output directory
+output_dir = Path("/home/zakaria/VIP/guillaume_data_test/derivatives/freesurfer")
+
+# List BASE and TP files from VIP 
+base_files = [
+    item['path']
+    for item in vip.list_elements(BASE_DIR)
+    if not item['isDirectory'] and item['path'].split('/')[-1].startswith("sub-") and "_TPs" not in item['path']
+]
+
+tp_files = [
+    item['path']
+    for item in vip.list_elements(TP_DIR)
+    if not item['isDirectory'] and item['path'].split('/')[-1].startswith("sub-") and "_TPs" in item['path']
+]
+
+# Match BASE → TP tarball 
+base_dict = {f.split("/")[-1].split(".")[0]: f for f in base_files}
+tp_dict   = {f.split("/")[-1].split("_TPs")[0]: f for f in tp_files}
+subjects = set(base_dict.keys()) & set(tp_dict.keys())
+
+if not subjects:
+    raise RuntimeError("No matching BASE and TP_TARBALL found!")
+
+print(f"Submitting {len(subjects)} LONG jobs for subjects: {', '.join(subjects)}")
+
+# Gather VIP input files per subject
+vip_input_files = []
+for sub in subjects:
+    vip_input_files.append(base_dict[sub])
+    vip_input_files.append(tp_dict[sub])
+
+# Input settings for the LONG pipeline
+input_settings = {
+    "LICENSE_FILE": LICENSE_FILE,
+    "BASE_ID": [base_dict[sub] for sub in subjects],      
+    "TP_TARBALL": [tp_dict[sub] for sub in subjects],   
+    "directives": "-all",                                
+}
+
+# Create VIP session
+session_name = "VIP_FS_LONG_parallel"
+session = VipSession(session_name)
+
+# Launch pipeline directly on VIP
+session.launch_pipeline(
+    pipeline_id="FreeSurfer-Recon-all-LONG/7.3.1",
+    input_settings=input_settings,
+    output_dir= str(output_dir)
+)
+
+# Monitor progress
+session.monitor_workflows()
+
+# Download outputs to the output_dir
+session.download_outputs(get_status=['Finished', 'Killed'])
+
+# Optional cleanup of outputs on VIP 
+# session.finish()
+

examples/freesurfer/freesurfer_longitudinal_processing/6-girder_upload_freesurfer_folder.py

@@ -0,0 +1,39 @@
+# Description:
+# Author: Frederic Cervenansky < frederic.cervenansky@creatis.insa-lyon.fr>
+#
+# Licence Cecill-B
+# Copyright (C) Creatis 2017-2024
+
+
+# import
+import girder_client
+import types
+import sys
+import click
+
+# api Rest url of the warehouse
+#Windows users: paths use backslashes (\) while Linux/macOS use forward slashes (/)
+url='https://insert/your-server-here/api/v1'
+# https://srmnopt.creatis.insa-lyon.fr/warehouse/api/v1 --> for NMR and Optics
+# https://myriad.creatis.insa-lyon.fr/api/v1 --> for MYRIAD
+
+# apiKey is a "mechanism" to share authentication and rights on folder.
+# User should defined through the web interface (inside user information) an apiKey with the corresponding privileges
+apiKey = 'GIRDER_API_KEY'
+
+# Generate the warehouse client
+gc = girder_client.GirderClient(apiUrl=url)
+
+# Authentication to the warehouse
+gc.authenticate(apiKey=apiKey)
+
+# upload local freesurfer folder in the original input folder on Girder
+folderId ='FOLDER_ID' #  3D Flow phantom+Bubbles
+#an example of a folder ID: 698de7fe82d062f2aea9619d
+
+# If 'derivatives' folder exists but 'freeSurfer' folder is absent:
+# gc.upload('/insert/your/upload/path/derivatives/freesurfer', folderId)
+
+# Default upload (if 'derivatives' folder is absent on the warehouse):
+gc.upload('/insert/your/upload/path/derivatives/', folderId)
+

examples/lcmodel/launch_lcmodel.ipynb

@@ -125,7 +125,7 @@
    "outputs": [],
    "source": [
     "# launch the execution and wait for it to finish\n",
-    "my_session.launch_pipeline(pipeline_id = \"LCModel/0.2-egi\", input_settings = input_settings)\n",
+    "my_session.launch_pipeline(pipeline_id = \"LCModel/0.6\", input_settings = input_settings)\n",
     "my_session.monitor_workflows()"
    ]
   },