Add daily traffic logging workflow and update permissions

.github/workflows/traffic_log.yml

@@ -0,0 +1,51 @@
+name: Log traffic stats
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+run-name: ${{ github.event_name }} - logging traffic stats
+
+on:
+  schedule:
+    - cron: 0 6 * * * # daily at 06:00 UTC
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  log-traffic:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - name: Checkout logging repo
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
+        with:
+          repository: markmikkelsen/gannet-traffic-log
+          token: ${{ secrets.TRAFFIC_LOG_TOKEN }}
+          path: log-repo
+
+      - name: Fetch traffic data
+        env:
+          GH_TOKEN: ${{ secrets.TRAFFIC_LOG_TOKEN }}
+        run: |
+          set -euo pipefail
+          mkdir -p log-repo/clones log-repo/views log-repo/releases
+          DATE=$(date -u +%Y-%m-%d)
+          gh api "repos/${{ github.repository }}/traffic/clones" \
+            > log-repo/clones/clones_$DATE.json
+          gh api "repos/${{ github.repository }}/traffic/views" \
+            > log-repo/views/views_$DATE.json
+          gh api "repos/${{ github.repository }}/releases" \
+            > log-repo/releases/releases_$DATE.json
+
+      - name: Commit and push
+        working-directory: log-repo
+        run: |
+          set -euo pipefail
+          git config user.name "traffic-bot"
+          git config user.email "actions@github.com"
+          git add .
+          git diff --quiet --cached || git commit -m "Traffic snapshot $(date -u +%Y-%m-%d)"
+          git push

.github/workflows/update_dependencies.yml

@@ -1,10 +1,10 @@
-name: Update dependencies - bids-matlab, dicm2nii, etc.
+name: Update dependencies
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-run-name: ${{ github.event_name }} - ${{ github.actor }} is updating dependencies
+run-name: ${{ github.event_name }} - updating dependencies
 
 on:
   schedule:

GEDeIdentify.m

@@ -234,7 +234,8 @@ function GEDeIdentify(fnames)
         fseek(pfile_fid, 1500, 'bof');
         hdr.series_offset = fread(pfile_fid, 1, 'integer*4');
     elseif rdbm_rev_num > 11.0
-        chkRev = {'14.3','16','20.006','20.007','24','26.002','27','27.001','28.002','28.003','30','30.1'};
+        chkRev = {'14.3','16','20.006','20.007','24','26.002','27', ...
+            '27.001','28.002','28.003','30','30.1','31'};
         if ~any(strcmp(num2str(rdbm_rev_num), chkRev))
             fclose(pfile_fid);
             fclose(pfile_fid_noID);
@@ -254,7 +255,8 @@ function GEDeIdentify(fnames)
                 rdb_hdr_da_yres       = 53;
                 rdb_hdr_dab_start_rcv = 101;
                 rdb_hdr_dab_stop_rcv  = 102;
-            case {'26.002','27','27.001','28.002','28.003','30','30.1'}
+            case {'26.002','27','27.001','28.002','28.003','30','30.1', ...
+                    '31'}
                 rdb_hdr_off_image     = 11;
                 rdb_hdr_off_data      = 2;
                 rdb_hdr_off_exam      = 9;

GERead.m

@@ -36,10 +36,12 @@
 end
 
 MRS_struct.p.GE.rdbm_rev_num(ii) = rdbm_rev_num;
-chkRev = {'14.3','16','20.006','20.007','24','26.002','27','27.001','28.002','28.003','30','30.1'};
+chkRev = {'14.3','16','20.006','20.007','24','26.002','27','27.001', ...
+    '28.002','28.003','30','30.1','31'};
 assert(any(strcmp(num2str(rdbm_rev_num), chkRev)), ...
     sprintf(['GERead.m is not fully functional with P-file header revision number %g. ' ...
-             'Please contact the Gannet developers (mam4041@med.cornell.edu) for assistance.'], ...
+    'Please open an issue on the Gannet GitHub repo ' ...
+    'for assistance: https://github.com/markmikkelsen/Gannet/issues'], ...
     rdbm_rev_num));
 
 % RTN 2018
@@ -175,7 +177,7 @@
         image_user22 = 112;
         image_user24 = 116;
 
-    case {'26.002','27','27.001','28.002','28.003','30','30.1'}
+    case {'26.002','27','27.001','28.002','28.003','30','30.1','31'}
 
         % int
         rdb_hdr_off_image   = 11;

GannetLoad.m

@@ -21,7 +21,7 @@
 
 MRS_struct.info.datetime.load = datetime('now');
 MRS_struct.info.version.Gannet = '3.5.4';
-MRS_struct.info.version.load = '260618';
+MRS_struct.info.version.load = '260814';
 MRS_struct.p.bids = 0;
 VersionCheck(0, MRS_struct.info.version.Gannet);
 ToolboxCheck;

GannetMask_GE.m

@@ -31,7 +31,7 @@
         tlhc                = 181;
         trhc                = 184;
         brhc                = 187;
-    case {'26.002','27','27.001','28.002','28.003','30','30.1'}
+    case {'26.002','27','27.001','28.002','28.003','30','30.1','31'}
         rdb_hdr_off_image   = 11;
         rdb_hdr_ps_mps_freq = 123;
         tlhc                = 181;

GannetMask_GE_nii.m

@@ -30,7 +30,7 @@
         tlhc                = 181;
         trhc                = 184;
         brhc                = 187;
-    case {'26.002','27','27.001','28.002','28.003','30','30.1'}
+    case {'26.002','27','27.001','28.002','28.003','30','30.1','31'}
         rdb_hdr_off_image   = 11;
         rdb_hdr_ps_mps_freq = 123;
         tlhc                = 181;

README.md

@@ -103,7 +103,7 @@ Gannet uses a form of [semantic versioning](https://semver.org/) in the style 'x
 
 ## Lead developer
 
-- Mark Mikkelsen (Weill Cornell Medicine)
+- Mark Mikkelsen
 
 ## Creator
 

SiemensTWIXRead.m

@@ -415,11 +415,10 @@
     % echo maximum in different fields, depending on the origin of the
     % sequence:
     if strcmp(TwixHeader.seqorig,'CMRR')
-        if strcmp(TwixHeader.seqtype,'MEGA-PRESS')
+        try
             TwixHeader.pointsBeforeEcho = twix_obj.image.iceParam(5,1);
-        elseif strcmp(TwixHeader.seqtype,'MEGA-sLASER') % SH 20191213
-            % TwixHeader.pointsBeforeEcho = twix_obj.image.freeParam(1);
-            TwixHeader.pointsBeforeEcho = twix_obj.image.iceParam(5,1); % MM (250805): This parameter may actually be the same as for the CMRR MEGA-PRESS WIP
+        catch
+            TwixHeader.pointsBeforeEcho = twix_obj.image.freeParam(1);
         end
     elseif strcmp(TwixHeader.seqorig,'WIP') % Siemens WIP
         TwixHeader.pointsBeforeEcho     = twix_obj.image.cutOff(1,1);

export_fig/crop_borders.m

@@ -26,6 +26,7 @@
 % 23/10/16: Fixed issue #175: there used to be a 1px minimal padding in case of crop, now removed
 % 15/05/22: Fixed EPS bounding box (issue #356)
 % 26/07/26: Fixed left edge auto-crop in Matlab R2025a+ (issue #408)
+% 13/08/26: Fixed bug when using positive (extra) padding parameter (PR #416)
 %}
 
     if nargin < 3
@@ -142,7 +143,12 @@
     if padding > 0  % extra padding
         % Create an empty image, containing the background color, that has the
         % cropped image size plus the padded border
-        B = repmat(bcol,[(b-t)+1+padding*2,(r-l)+1+padding*2,1,n]);  % Fix per Luiz Carvalho
+        nRows = b-t+1 + padding*2;
+        nCols = r-l+1 + padding*2;
+        %B = repmat(bcol, [nRows,nCols,1,n]);  % Fix per Luiz Carvalho
+        B(1:nRows, 1:nCols, 3, 1:n) = bcol(3); % Fix PR #416
+        B(1:nRows, 1:nCols, 2, 1:n) = bcol(2); % Fix PR #416
+        B(1:nRows, 1:nCols, 1, 1:n) = bcol(1); % Fix PR #416
         % vA - coordinates in A that contain the cropped image
         vA = [t b l r];
         % vB - coordinates in B where the cropped version of A will be placed

export_fig/export_fig.m

@@ -419,6 +419,7 @@
 % 01/06/26: (3.55) Fixes for exporting uifigures in Matlab R2025a+ (issue #408)
 % 22/07/26: (3.56) Suppress some warnings/alerts if -silent option specified or in parallel/batch mode (issue #415); added default comment in GIF/JPG/PNG/TIF images; try to create export folder if it does not exist
 % 26/07/26: (3.57) Fixed unintended figure undock, bgcolor and bad auto-cropping in Matlab R2025a+ (issue #408)
+% 13/08/26: (3.58) Fixed TIF export bug; fixed bug when using -p (extra padding/cropping) parameter; improved parsing of parameter-value input pairs
 %}
 
     if nargout
@@ -457,7 +458,7 @@
     [fig, options] = parse_args(nargout, fig, argNames, varargin{:});
 
     % Check for newer version and exportgraphics/copygraphics compatibility
-    currentVersion = 3.57;
+    currentVersion = 3.58;
     if options.version  % export_fig's version requested - return it and bail out
         imageData = currentVersion;
         return
@@ -1023,7 +1024,7 @@
                     format_options = getFormatOptions(options, 'tif');  %Issue #269
                     default_options = {'Resolution',resolution, 'WriteMode',mode, ...
                                        'Description',createdUsing};
-                    imwrite(img, filename, default_options, format_options{:});
+                    imwrite(img, filename, default_options{:}, format_options{:});
                 end
                 if options.notify, notify(filename); end
             end
@@ -2106,12 +2107,16 @@ function notify(filename)
                                     case 's', options.fixed_size = vals;
                                 end
                             else  % scalar parameter value
-                                val = str2double(regexpi(thisArg, '(?<=-([mrqp]))-?\d*.?\d+', 'match'));
+                                val = str2double(regexpi(thisArg, '(?<=-([mrqp]))\s*-?\d*.?\d+', 'match'));
                                 if isempty(val) || isnan(val)
-                                    % Issue #51: improved processing of input args (accept space between param name & value)
-                                    val = str2double(varargin{a+1});
-                                    if isscalar(val) && ~isnan(val)
-                                        skipNext = 1;
+                                    if ~isempty(extra)
+                                        val = str2double(extra(2:end));
+                                    else
+                                        % Issue #51: improved processing of input args (accept space between param name & value)
+                                        val = str2double(varargin{a+1});
+                                        if isscalar(val) && ~isnan(val)
+                                            skipNext = 1;
+                                        end
                                     end
                                 end
                                 if ~isscalar(val) || isnan(val)