Merge branch 'main' of github.com:openneuropet/PET2BIDS into 319-standardize-radiochemistry-metadata-caseorder

Author: bendhouseart

.github/workflows/phantoms.yaml

@@ -67,12 +67,6 @@ jobs:
             brew install dcm2niix
           fi
 
-      - name: Debug
-        uses: mxschmitt/action-tmate@v3
-        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
-        timeout-minutes: 15
-        with:
-          limit-access-to-actor: true
 
       - name: Check dcm2niix is installed and on path
         if: runner.os != 'Windows'
@@ -106,10 +100,10 @@ jobs:
           dcm2niix4pet -h
 
       - name: Set Up Node
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
 
       - name: Install BIDS Validator
-        run: npm install -g bids-validator
+        run: npm install -g bids-validator@1.14.6
 
       - name: Collect Phantoms
         if: ${{ steps.cache-phantoms.outputs.cache-hit != 'true' }} && ${{ !env.ACT }}
@@ -170,6 +164,13 @@ jobs:
         run: |
           bids-validator OpenNeuroPET-Phantoms/python
 
+      - name: Debug
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+        timeout-minutes: 15
+        with:
+          limit-access-to-actor: true
+
       - name: Validate Matlab Conversion
         run: |
           bids-validator OpenNeuroPET-Phantoms/matlab

README.md

@@ -4,6 +4,9 @@
 [![Matlab PET2BIDS Tests](https://github.com/openneuropet/PET2BIDS/actions/workflows/matlab.yaml/badge.svg)](https://github.com/openneuropet/PET2BIDS/actions/workflows/matlab.yaml) 
 [![Documentation Status](https://readthedocs.org/projects/pet2bids/badge/?version=latest)](https://pet2bids.readthedocs.io/en/latest/?badge=latest)
 [![phantoms](https://github.com/openneuropet/PET2BIDS/actions/workflows/phantoms.yaml/badge.svg)](https://github.com/openneuropet/PET2BIDS/actions/workflows/phantoms.yaml)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06067/status.svg)](https://doi.org/10.21105/joss.06067)
+
+Galassi, A., Norgaard, M., Gonzalez-Escamilla, G., Svarer, C., Rorden, C., Matheson, G.J, Knudsen, G.M, Innis, R.B., Ganz, M., Eierud, C., Bilgel., M. & Pernet, C. (2024). PET2BIDS: a library for converting Positron Emission Tomography data to BIDS. Journal of Open Source Software, 9(100), 6067.
 
 This repository is hosting tools to curate PET brain data using the [Brain Imaging Data Structure Specification](https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/09-positron-emission-tomography.html). 
 The work to create these tools is funded by [Novo Nordisk Foundation](https://novonordiskfonden.dk/en/) (NNF20OC0063277) and the 

docs/spreadsheets.rst

@@ -14,14 +14,14 @@ dedicated to the topic of spreadsheets and PET blood/radioligand/radioactivity d
 Handled Types of Spreadsheets (known)
 -------------------------------------
 
-`link to repository section <https://github.com/OpenNeuroPET/PET2BIDS/spreadsheet_conversion>`_
+`link to repository section <https://github.com/openneuropet/PET2BIDS/tree/main/spreadsheet_conversion>`_
 
 **Excel**
 
-- `Ideal single subject example <https://github.com/OpenNeuroPET/PET2BIDS/spreadsheet_conversion/single_subject_sheet/subject_metadata_example.xlsx>`_
+- `Ideal single subject example <https://github.com/openneuropet/PET2BIDS/raw/refs/heads/main/spreadsheet_conversion/single_subject_sheet/subject_metadata_example.xlsx>`_
 - Here is an example of a
-  `Many Subject Spreadsheet <https://github.com/OpenNeuroPET/PET2BIDS/spreadsheet_conversion/many_subjects_sheet/subjects_metadata_example.xlsx>`_
-  paired with a `single subject spreadsheet  <https://github.com/OpenNeuroPET/PET2BIDS/spreadsheet_conversion/many_subjects_sheet/subject_>`_
+  `Many Subject Spreadsheet <https://github.com/openneuropet/PET2BIDS/raw/refs/heads/main/spreadsheet_conversion/many_subjects_sheet/scanner_metadata_example.xlsx>`_
+  paired with a `single subject spreadsheet  <https://github.com/openneuropet/PET2BIDS/raw/refs/heads/main/spreadsheet_conversion/many_subjects_sheet/subjects_metadata_example.xlsx>`_
   these can be used when updating BIDS datasets w/ homogeneous scanner/experiment data along with heterogeneous (subject)
   data.
 

matlab/dcm2niix4pet.m

@@ -30,7 +30,7 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
 %   - *w*          = 2;      % write behavior for name conflicts (0,1,2, default 2: 0=skip duplicates, 1=overwrite, 2=add suffix)
 %   - *x*          = 'n';    % crop 3D acquisitions (y/n/i, default n, use 'i'gnore to neither crop nor rotate 3D acquisitions)
 %   - *z*          = 'n';    % gz compress images (y/o/i/n/3, default y) [y=pigz, o=optimal pigz, i=internal:miniz, n=no, 3=no,3D]
-% :param notrack: boolean to Opt-out of sending tracking information of this run to the PET2BIDS developers. This information helps to improve PET2BIDS and provides an indicator of real world usage crucial for obtaining funding."
+%  - *notrack* Opt-out of sending tracking information of this run to the PET2BIDS developers. This information helps to improve PET2BIDS and provides an indicator of real world usage crucial for obtaining funding."
 %
 % .. code-block::
 %
@@ -69,13 +69,13 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
 version = regexp(version_output_string, 'v[0-9].[0-9].{8}[0-9]', 'match');
 
 
-% initalize telemetry data fror later uploading
+% initialize telemetry data fror later uploading
 telemetry_data = {};
 dcm2niix_data = {};
 dcm2niix_data.version = version(1);
 dcm2niix_data.returncode = 0;
 telemetry_data.dcm2niix = dcm2niix_data;
-telemetry_data.description = "Matlab_dcm2niix4pet.m"
+telemetry_data.description = "Matlab_dcm2niix4pet.m";
 
 if length(version) >= 1
     version_date = version{1}(6:end);
@@ -222,8 +222,6 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
         outputdir = varargin{var+1};
     elseif strcmpi(varargin{var},'notrack')
         setenv('TELEMETRY_ENABLED', 'False')
-    else
-        error('unknown option %s',varargin{var})
     end
 
 end
@@ -241,8 +239,6 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
     end
 end
 
-
-
 %% convert
 % ----------
 for folder = 1:size(FolderList,1)
@@ -273,10 +269,8 @@ function dcm2niix4pet(FolderList,MetaList,varargin)
         telemetry_data.returncode = 1;
         telemetry(telemetry_data, folder);
         error('%s did not run properly',command)
-        
     end
-
-
+   
     % deal with dcm files
     dcmfiles = dir(fullfile(FolderList{folder},'*.dcm'));
     if isempty(dcmfiles) % since sometimes they have no ext :-(

matlab/telemetry.m

@@ -18,10 +18,13 @@ function telemetry(telemetry_data, input_path, output_path)
             telemetry_data.TotalInputFileSize = input_file_count.TotalInputFileSize;
         end
 
-        url = 'http://52.87.154.236/telemetry/';
-        options = weboptions('MediaType', 'application/json');
-        response = webwrite(url, telemetry_data, options);
-
+        url = 'http://openneuropet.org/pet2bids/';
+        options = weboptions('MediaType', 'application/json', 'Timeout', 5);
+        try
+            response = webwrite(url, telemetry_data, options);
+        catch ME
+            % do nothing
+        end
     else
         % don't do anything
     end
@@ -46,8 +49,11 @@ function telemetry(telemetry_data, input_path, output_path)
     end
 
     disable_telemetry = strcmpi(getenv("TELEMETRY_ENABLED"), 'false');
-    
-    if disable_telemetry | disable_telemetry_env
+
+    % if running in CI don't run telemetry
+    running_in_ci = strcmpi(getenv("CI"), 'true');
+
+    if disable_telemetry | disable_telemetry_env | running_in_ci
         e = false;
     else
         e = true;