MELDProject · mathrip · Apr 24, 2026 · May 30, 2025 · Oct 3, 2025 · Oct 15, 2025
diff --git a/Dockerfile b/Dockerfile
@@ -10,6 +10,10 @@ RUN rm /opt/hippunfold_cache/trained_model.3d_fullres.Task102_hcp1200_T2w.nnUNet
 
 # Update OS and install prerequisite
 ENV DEBIAN_FRONTEND="noninteractive"
+# Use archived repositories for Debian Buster (since it's EOL)
+RUN sed -i 's|http://deb.debian.org/debian|http://archive.debian.org/debian|g' /etc/apt/sources.list && \
+	sed -i 's|http://security.debian.org/debian-security|http://archive.debian.org/debian-security|g' /etc/apt/sources.list && \
+	sed -i '/buster-updates/d' /etc/apt/sources.list
 RUN apt-get --allow-releaseinfo-change update
 RUN apt-get install -y python3-pip \
 	time \
@@ -38,6 +42,9 @@ RUN cd /app/ && conda run -n base /bin/bash -c "pip install -e ."
 # Set permissions for the entrypoint
 RUN chmod +x entrypoint.sh
 
+ENV KEEP_DATA_PATH=1
+ENV SILENT=1
+
 ENTRYPOINT ["/bin/bash","entrypoint.sh"]
 
 
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,131 @@
+# PolyForm Noncommercial License 1.0.0
+
+<https://polyformproject.org/licenses/noncommercial/1.0.0>
+
+## Acceptance
+
+In order to get any license under these terms, you must agree
+to them as both strict obligations and conditions to all
+your licenses.
+
+## Copyright License
+
+The licensor grants you a copyright license for the
+software to do everything you might do with the software
+that would otherwise infringe the licensor's copyright
+in it for any permitted purpose.  However, you may
+only distribute the software according to [Distribution
+License](#distribution-license) and make changes or new works
+based on the software according to [Changes and New Works
+License](#changes-and-new-works-license).
+
+## Distribution License
+
+The licensor grants you an additional copyright license
+to distribute copies of the software.  Your license
+to distribute covers distributing the software with
+changes and new works permitted by [Changes and New Works
+License](#changes-and-new-works-license).
+
+## Notices
+
+You must ensure that anyone who gets a copy of any part of
+the software from you also gets a copy of these terms or the
+URL for them above, as well as copies of any plain-text lines
+beginning with `Required Notice:` that the licensor provided
+with the software.  For example:
+
+> Required Notice: Copyright Yoyodyne, Inc. (http://example.com)
+
+## Changes and New Works License
+
+The licensor grants you an additional copyright license to
+make changes and new works based on the software for any
+permitted purpose.
+
+## Patent License
+
+The licensor grants you a patent license for the software that
+covers patent claims the licensor can license, or becomes able
+to license, that you would infringe by using the software.
+
+## Noncommercial Purposes
+
+Any noncommercial purpose is a permitted purpose.
+
+## Personal Uses
+
+Personal use for research, experiment, and testing for
+the benefit of public knowledge, personal study, private
+entertainment, hobby projects, amateur pursuits, or religious
+observance, without any anticipated commercial application,
+is use for a permitted purpose.
+
+## Noncommercial Organizations
+
+Use by any charitable organization, educational institution,
+public research organization, public safety or health
+organization, environmental protection organization,
+or government institution is use for a permitted purpose
+regardless of the source of funding or obligations resulting
+from the funding.
+
+## Fair Use
+
+You may have "fair use" rights for the software under the
+law. These terms do not limit them.
+
+## No Other Rights
+
+These terms do not allow you to sublicense or transfer any of
+your licenses to anyone else, or prevent the licensor from
+granting licenses to anyone else.  These terms do not imply
+any other licenses.
+
+## Patent Defense
+
+If you make any written claim that the software infringes or
+contributes to infringement of any patent, your patent license
+for the software granted under these terms ends immediately. If
+your company makes such a claim, your patent license ends
+immediately for work on behalf of your company.
+
+## Violations
+
+The first time you are notified in writing that you have
+violated any of these terms, or done anything with the software
+not covered by your licenses, your licenses can nonetheless
+continue if you come into full compliance with these terms,
+and take practical steps to correct past violations, within
+32 days of receiving notice.  Otherwise, all your licenses
+end immediately.
+
+## No Liability
+
+***As far as the law allows, the software comes as is, without
+any warranty or condition, and the licensor will not be liable
+to you for any damages arising out of these terms or the use
+or nature of the software, under any kind of legal claim.***
+
+## Definitions
+
+The **licensor** is the individual or entity offering these
+terms, and the **software** is the software the licensor makes
+available under these terms.
+
+**You** refers to the individual or entity agreeing to these
+terms.
+
+**Your company** is any legal entity, sole proprietorship,
+or other kind of organization that you work for, plus all
+organizations that have control over, are under the control of,
+or are under common control with that organization.  **Control**
+means ownership of substantially all the assets of an entity,
+or the power to direct its management and policies by vote,
+contract, or otherwise.  Control can be direct or indirect.
+
+**Your licenses** are all the licenses granted to you for the
+software under these terms.
+
+**Use** means anything you do with the software requiring one
+of your licenses.
diff --git a/README.md b/README.md
@@ -13,12 +13,8 @@ Note:
 - You will need the following demographic information (age at scan & sex) to run AID-HS on your patient's T1 MRI scan.
 - AID-HS has been developed on T1w scans acquired at 3T. It has not yet been thoroughly evaluated on 1.5T and 7T data
 
-**<span style="color: red;">SIGN UP TO THE AID-HS MAILING LIST</span>**:
-We request that all AID-HS users sign up to the mailing list. If you are using AID-HS, please send an email to `meld.study@gmail.com` with the subject 'Request to be added to the AID-HS mailing list' and provide use with your name and institute. This will ensure that we can update you about bug fixs and new releases. 
-
-**<span style="color: red;">EXISTING USERS: PLEASE UPDATE TO VERSION V1.0.1</span>**:
-We have released AID-HS V1.0.1 which fixes a couple of issues found by users. For more information about the release please see [AID-HS V1.0.1](https://github.com/MELDProject/AID-HS/releases/tag/v1.0.1). To update your code please follow the guidelines [Updating AID-HS to V1.0.1](https://aid-hs.readthedocs.io/en/latest/FAQs.html#Updating-AID-HS-to-V1.0.1) from our FAQ.
-
+**<span style="color: red;">REGISTER TO GET YOUR AID-HS LICENSE</span>**:
+We request that all AID-HS users fill the [AID-HS registration form](https://docs.google.com/forms/d/e/1FAIpQLSdPbtraBZ2s0HD1W8qtF11wr_fYVTWZjraED03Rtl2ZjxeRMA/viewform?usp=header). Following registration you will received a license file. This file will be needed for use of all future AID-HS versions v1.1.0 and above. Your email address will be added to the AID-HS mailing list. This will ensure that we can update you about bugs fix and new releases. 
 
 Pipeline overview:\
 <img src="https://raw.githubusercontent.com//MELDProject/AID-HS/main/docs/images/overview_pipeline.jpg " height="500" />
@@ -36,6 +32,7 @@ You can install and use the AID-HS pipeline with :
 - [**native installation**](https://aid-hs.readthedocs.io/en/latest/install_native.html): Not supported 
 
 **YouTube tutorial available for the [docker and singularity installation](https://www.youtube.com/watch?v=RRAET7r05ys&t=11s&ab_channel=MELDproject)**
+Note: for installation, please follow the online guidelines on github which are up to date compare to the videos
 
 **FAQs** 
 If you have a question or if you are running into issues at any stage (installation/use/interpretation), have a look at our [FAQs](https://aid-hs.readthedocs.io/en/latest/FAQs.html) page as we may have already have a solution. 
@@ -56,7 +53,7 @@ Once installed you will be able to use the AID-HS pipeline on your data followin
 Features extracted from MRI scans from different MRI scanners have systematic differences between them. To remove scanner related biases we recommend harmonising your MRI data to the MRI data that was used in the AID-HS manuscript. This harmonisation is required for each MRI scanner / T1 sequence you are using. 
 
 Notes: 
-- This step needs to be run only once, and requires data from at least 20 subjects acquired on the same scanner with the same T1 sequence and demographic information (e.g age and sex). See [harmonisation instructions](https://aid-hs.readthedocs.io/en/latest/harmonisation.html) for more details. 
+- This step needs to be run only once, and requires data from at least 20 controls acquired on the same scanner with the same T1 sequence and demographic information (e.g age and sex). See [harmonisation instructions](https://aid-hs.readthedocs.io/en/latest/harmonisation.html) for more details. 
 - The AID-HS pipeline can also be run without harmonisation with no drop in performances. However, the characterisation of the hippocampal features compared to the normative growth curves will not be interpretable.
 
 
@@ -69,7 +66,10 @@ An overview of the notebooks that we used to create the figures can be found [he
 
 ## Contacts
 
-Mathilde Ripart, PhD \ 
+MELD project\
+`meld.study@gmail.com`
+
+Mathilde Ripart, PhD \
 Research Fellow at UCL Great Ormond Street Institute of Child Health \
 `m.ripart@ucl.ac.uk` 
 
@@ -80,3 +80,5 @@ Research Fellow at UCL Great Ormond Street Institute of Child Health \
 
 
 
+
+
diff --git a/aidhs/__init__.py b/aidhs/__init__.py
@@ -1,3 +1,3 @@
 __author__ = __maintainer__ = "Mathilde Ripart"
 __email__ = "m.ripart@ucl.ac.uk"
-__version__ = "1.0.1"
+__version__ = "1.1.0"
diff --git a/aidhs/aidhs_cohort_hip.py b/aidhs/aidhs_cohort_hip.py
@@ -254,7 +254,7 @@ def get_sites(self):
         sites = []
         for f in glob.glob(os.path.join(self.data_dir, "AIDHS_*")):
             if os.path.isdir(f):
-                sites.append(f.split("_")[-1])
+                sites.append(f.split("AIDHS_")[-1])
         return sites
 
     @contextmanager

diff --git a/aidhs/data_preprocessing.py b/aidhs/data_preprocessing.py
@@ -201,7 +201,6 @@ def load_covars(self, subject_ids=None, demographic_file=DEMOGRAPHIC_FEATURES_FI
         covars = pd.DataFrame()
         ages = []
         sex = []
-        group = []
         sites_scanners = []
         for subject in subject_ids:
             subj = AidhsSubject(subject, cohort=self.cohort)
@@ -215,12 +214,10 @@ def load_covars(self, subject_ids=None, demographic_file=DEMOGRAPHIC_FEATURES_FI
                 sex.append(s)
             else:
                 print(f'ERROR: There is an issue with the coded sex of subject {subject}')
-            group.append(subj.is_patient)
             sites_scanners.append(subj.site_code) # just site code now
 
         covars["ages"] = ages
         covars["sex"] = sex
-        covars["group"] = group
         covars["site_scanner"] = sites_scanners
         covars["ID"] = subject_ids
 
@@ -497,7 +494,7 @@ def combat_whole_cohort(self, feature_name, outliers_file=None, combat_params_fi
         print(f"INFO: exclude subjects {np.array(self.subject_ids)[~combat_subject_include]}")
         if precombat_features:
             precombat_features = np.array(precombat_features)
-            # load in covariates - age, sex, group, site and scanner unless provided
+            # load in covariates - age, sex, site and scanner unless provided
             covars = self.covars[combat_subject_include].copy()
             # check for nan
             index_nan = pd.isnull(covars).any(1).to_numpy().nonzero()[0]
@@ -518,7 +515,7 @@ def combat_whole_cohort(self, feature_name, outliers_file=None, combat_params_fi
                         precombat_features.T,
                         covars,
                         batch_col="site_scanner",
-                        categorical_cols=["sex", "group"],
+                        categorical_cols=["sex"],
                         continuous_cols="ages",
                     )
                     #
@@ -579,7 +576,7 @@ def get_combat_new_site_parameters(self,feature, demographic_file,):
         if len(np.array(listids)[np.array(combat_subject_include)])==0:
             print(f'Cannot compute harmonisation for {feature} because no subject found with this feature')
             return
-        # load in covariates - age, sex, group, site and scanner unless provided    
+        # load in covariates - age, sex, site and scanner unless provided    
         new_site_covars = self.load_covars(subject_ids=np.array(listids)[np.array(combat_subject_include)], demographic_file=demographic_file).copy()
         #check site_scanner codes are the same for all subjects
         if len(new_site_covars['site_scanner'].unique())==1:
@@ -595,7 +592,7 @@ def get_combat_new_site_parameters(self,feature, demographic_file,):
         new_site_data = np.array(precombat_features).T 
         dc.distributedCombat_site(new_site_data,
                                   bat, 
-                                  new_site_covars[['ages','sex','group']], 
+                                  new_site_covars[['ages','sex']], 
                                   file=os.path.join(site_combat_path,f"{site_code}_{feature}_summary.pickle"), 
                               ref_batch = 'H0', 
                               robust=True,)
@@ -606,12 +603,12 @@ def get_combat_new_site_parameters(self,feature, demographic_file,):
         )
         # third, use variance estimates from full AIDHS cohort
         dc_out['var_pooled'] = pd.read_pickle(os.path.join(aidhs_combat_path,f'combat_{feature}_var.pickle')).ravel()
-        for c in ['ages','sex','group']:
+        for c in ['ages','sex']:
             new_site_covars[c]=new_site_covars[c].astype(np.float64)      
         print('step3')
         pickle_file = os.path.join(site_combat_path,f"{site_code}_{feature}_harmonisation_params_test.pickle")
         _=dc.distributedCombat_site(
-            pd.DataFrame(new_site_data), bat, new_site_covars[['ages','sex','group']], 
+            pd.DataFrame(new_site_data), bat, new_site_covars[['ages','sex']], 
             file=pickle_file,
              central_out=dc_out, 
             ref_batch = 'H0', 

diff --git a/aidhs/download_data.py b/aidhs/download_data.py
@@ -0,0 +1,40 @@
+import urllib.request
+import os
+import numpy as np
+from aidhs.paths import DATA_PATH
+import sys
+import shutil
+import tempfile
+
+def _fetch_url(url, fname):
+    def dlProgress(count, blockSize, totalSize):
+        percent = int(count*blockSize*100/totalSize)
+        if not "SILENT" in os.environ:
+            sys.stdout.write("\r" + url + "...%d%%" % percent)
+            sys.stdout.flush()
+    return urllib.request.urlretrieve(url, fname, reporthook=dlProgress)
+
+
+def download_aidhs_data(aidhs_data_path=DATA_PATH):
+    """
+    download AID-HS data from GitHub release: model, parameters and test data 
+    """
+    url = "https://github.com/MELDProject/AID-HS/releases/download/aidhs_data/aidhs_data.zip"
+    with tempfile.TemporaryDirectory() as tmpdirname:
+        # download to tmpdir
+        _fetch_url(url, os.path.join(tmpdirname, "aidhs_data_folder.zip"))
+        # unpack
+        shutil.unpack_archive(os.path.join(tmpdirname, "aidhs_data_folder.zip"), aidhs_data_path)
+    print(f"\ndownloaded AID-HS data to {aidhs_data_path}")
+
+def check_data(force_download=False):
+    for folder in ['input','output','models','params']:
+        exit = False
+        if os.path.exists(os.path.join(DATA_PATH, folder)):
+            print(f'The folder {folder} already exists at {DATA_PATH}.')
+            exit = True
+    if force_download:
+        print('Data to download already (partially) exists. \nData will be overwritten.') 
+    if exit and (force_download==False):
+        print('Data to download already (partially) exists. \nDownload aborted. Please delete folders or provide a new path.')
+        sys.exit()
diff --git a/aidhs/paths.py b/aidhs/paths.py
@@ -57,7 +57,7 @@
 
 
 # paths to important data files - relative to BASE_PATH
-DEMOGRAPHIC_FEATURES_FILE = os.path.join(DATA_PATH, "demographics_file.csv")
+DEMOGRAPHIC_FEATURES_FILE = f"/tmp/demographics_file_{os.getpid()}.csv"
 
 # params file
 CLIPPING_PARAMS_FILE='clipping_parameters_sigma.json'

diff --git a/aidhs/test/test_aidhs_license.py b/aidhs/test/test_aidhs_license.py
@@ -0,0 +1,31 @@
+import os
+import sys
+import re
+from pathlib import Path
+
+def test_license():
+
+    # Get the meld license variable
+    aidhs_license_file = os.getenv("AIDHS_LICENSE", None)
+
+    if aidhs_license_file is None: 
+        print('ERROR: Could not find a AIDHS_LICENSE environment variable. Please ensure you have exported the AIDHS_LICENSE environment following the AID-HS installation guidelines')
+        sys.exit()
+    if not os.path.isfile(aidhs_license_file): 
+        print(f'ERROR: The file {aidhs_license_file} does not exist.\nPlease ensure you got the meld license file by filling the registration form provided in the AID-HS installation guidelines and provided the right path to the file')
+        sys.exit()
+
+    # check that the license is correct
+    text = Path(aidhs_license_file).read_text()
+    m = re.search(r"License\s*ID[:\s]*([0-9]+)", text, re.IGNORECASE)
+    if m:
+        license_id = m.group(1)
+        if not len(license_id) == 6:
+            print("ERROR: The license ID provided does not seem correct.\nPlease ensure you got the correct meld license file by filling the registration form provided in the AID-HS installation guidelines and provided the right path to the file")
+            sys.exit()
+    else:
+        print(f"ERROR: The license file {aidhs_license_file} does not seem correct.\nPlease ensure you got the correct meld license file by filling the registration form provided in the AID-HS installation guidelines and provided the right path to the file")
+        sys.exit()
+
+# call the test
+test_license()  
diff --git a/compose.yml b/compose.yml
@@ -1,9 +1,13 @@
 services:
   aidhs:
-    image: meldproject/aidhs:latest
+    image: meldproject/aidhs:v1.1.0
     platform: "linux/amd64"
     volumes:
       - volumes:/data
+    environment: 
+      - AIDHS_LICENSE=/run/secrets/aidhs_license.txt
+    secrets:
+      - aidhs_license.txt
     user: $DOCKER_USER
     deploy:
       resources:
@@ -12,3 +16,7 @@ services:
             - capabilities: [gpu]
               count: 0
 
+secrets:
+  aidhs_license.txt:
+    file: ./aidhs_license.txt
+