Merge branch 'Deep-MI:dev' into dev

.github/workflows/doc.yml

@@ -41,7 +41,8 @@ jobs:
             !doc-build/.doctrees
 
   deploy:
-    if: github.event_name == 'push'
+    # only on push to dev or stable
+    if: ${{ github.event_name == 'push' && contains(fromJSON('["dev", "stable"]'), github.ref_name) }}
     needs: build
     timeout-minutes: 10
     runs-on: ubuntu-latest
@@ -56,12 +57,12 @@ jobs:
         with:
           name: doc
           path: doc
-      - name: Deploy dev documentation
+      - name: Deploy {dev,stable} documentation
         uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: doc
-          # destination_dir: github.event.ref_name will be dev or stable
-          destination_dir: ${{ github.event.ref_name }}
+          # destination_dir: github.ref_name will be dev or stable
+          destination_dir: ${{ github.ref_name }}
           user_name: 'github-actions[bot]'
           user_email: 'github-actions[bot]@users.noreply.github.com'

Docker/Dockerfile

@@ -162,6 +162,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Add FreeSurfer and python Environment variables
+# DO_NOT_SEARCH_FS_LICENSE_IN_FREESURFER_HOME=true deactivates the search for FS_LICENSE in FREESURFER_HOME
 ENV OS=Linux \
     FS_OVERRIDE=0 \
     FIX_VERTEX_AREA="" \
@@ -171,7 +172,8 @@ ENV OS=Linux \
     PYTHONUNBUFFERED=0 \
     MPLCONFIGDIR=/tmp \
     PATH=/venv/bin:/opt/freesurfer/bin:$PATH \
-    MPLCONFIGDIR=/tmp/matplotlib-config
+    MPLCONFIGDIR=/tmp/matplotlib-config \
+    DO_NOT_SEARCH_FS_LICENSE_IN_FREESURFER_HOME="true"
 
 # create matplotlib config dir; make sure we use bash and activate conda env
 #  (in case someone starts this interactively)

HypVINN/inference.py

@@ -320,7 +320,7 @@ def eval(self, val_loader: DataLoader, pred_prob: torch.Tensor, out_scale: float
 
             images = batch["image"].to(self.device)
             scale_factors = batch["scale_factor"].to(self.device)
-            weight_factors = batch["weight_factor"].to(self.device)
+            weight_factors = batch["weight_factor"].to(self.device, dtype=torch.float32)
 
             pred = self.model(images, scale_factors, weight_factors, out_scale)
 

HypVINN/utils/stats_utils.py

@@ -71,5 +71,7 @@ def compute_stats(
     args.patch_size = 32
     args.device = "auto"
     args.lut = FASTSURFER_ROOT / "FastSurferCNN/config/FreeSurferColorLUT.txt"
-    args.allow_root = False
+    # We check for this in the parent code
+    # TODO: it would be better to populate this properly
+    args.allow_root = True
     return main(args)

recon_surf/recon-surf.sh

@@ -389,7 +389,7 @@ echo "Log file for Conform test" > "$CONFORM_LF"
 
 # check for input conformance
 cmd="$python $FASTSURFER_HOME/FastSurferCNN/data_loader/conform.py -i $t1 --check_only --vox_size min --verbose"
-RunIt "$cmd" "$LF" |& tee -a "$CONFORM_LF"
+RunIt "$cmd" "$LF" 2>&1 | tee -a "$CONFORM_LF"
 
 # look into the CONFORM_LF to find the voxel sizes, the second conform.py call will check the legality of vox_size
 vox_size=$(grep -E " - Voxel Size " "$CONFORM_LF" | cut -d' ' -f5 | cut -d'x' -f1)
@@ -835,7 +835,7 @@ if [ "$DoParallel" == 1 ] ; then
     echo ""
     echo " RUNNING HEMIs in PARALLEL !!! "
     echo ""
-  } |& tee -a "$LF"
+  } | tee -a "$LF"
   RunBatchJobs "$LF" "${CMDFS[@]}"
 fi
 
@@ -1088,7 +1088,7 @@ tRunHours=$(printf %6.3f "$tRunHours")
   echo "Started at $StartTime"
   echo "Ended   at $EndTime"
   echo "#@#%# recon-surf-run-time-hours $tRunHours"
-} |& tee -a "$LF"
+} | tee -a "$LF"
 
 # Create the Done File
 {
@@ -1113,7 +1113,7 @@ tRunHours=$(printf %6.3f "$tRunHours")
   echo "CMDPATH $0"
   echo "CMDARGS ${inputargs[*]}"
 } > "$DoneFile"
-echo "recon-surf.sh $subject finished without error at $(date)"  |& tee -a "$LF"
+echo "recon-surf.sh $subject finished without error at $(date)" | tee -a "$LF"
 
 cmd="$python ${binpath}utils/extract_recon_surf_time_info.py -i $LF -o $SUBJECTS_DIR/$subject/scripts/recon-surf_times.yaml"
 RunIt "$cmd" "/dev/null"

recon_surf/smooth_aparc.py

@@ -212,8 +212,8 @@ def mode_filter(
     # get rid of rows that have uniform vote (or are empty)
     # for this to work no negative numbers should exist
     # get row counts, max and sums
-    rmax = nlabels.max(1).A.squeeze()
-    sums = nlabels.sum(axis=1).A1
+    rmax = nlabels.max(1).toarray().squeeze()
+    sums = np.asarray(nlabels.sum(axis=1)).ravel()
     counts = np.diff(nlabels.indptr)
     # then keep rows where max*counts differs from sums
     rmax = np.multiply(rmax, counts)
@@ -224,7 +224,7 @@ def mode_filter(
     # since we have only rows that were non-uniform, they should not become empty
     # rows may become unform: we still need to vote below to update this label
     if novote:
-        rr = np.in1d(nlabels.data, novote)
+        rr = np.isin(nlabels.data, novote)
         nlabels.data[rr] = 0
         nlabels.eliminate_zeros()
     # run over all rows and compute mode (maybe vectorize later)
@@ -303,7 +303,7 @@ def smooth_aparc(surf, labels, cortex = None):
     noncortids = np.where(~mask)
 
     # remove triangles where one vertex is non-cortex to avoid these edges to vote on neighbors later
-    rr = np.in1d(faces, noncortids)
+    rr = np.isin(faces, noncortids)
     rr = np.reshape(rr, faces.shape)
     rr = np.amax(rr, 1)
     faces = faces[~rr, :]
@@ -342,7 +342,7 @@ def smooth_aparc(surf, labels, cortex = None):
             )
             fillids = np.where(labels == fillonlylabel)[0]
             labels[fillids] = 0
-            rr = np.in1d(faces, fillids)
+            rr = np.isin(faces, fillids)
             rr = np.reshape(rr, faces.shape)
             rr = np.amax(rr, 1)
             faces = faces[~rr, :]

run_fastsurfer.sh

@@ -697,8 +697,24 @@ then
   msg="The surface pipeline and the talairach-registration in the segmentation pipeline require a FreeSurfer License"
   if [[ -z "$FS_LICENSE" ]]
   then
-    echo "ERROR: $msg, but no license was provided via --fs_license or the FS_LICENSE environment variable."
-    exit 1;
+    msg="$msg, but no license was provided via --fs_license or the FS_LICENSE environment variable."
+    if [[ "$DO_NOT_SEARCH_FS_LICENSE_IN_FREESURFER_HOME" != "true" ]] && [[ -n "$FREESURFER_HOME" ]]
+    then
+      echo "WARNING: $msg Checking common license files in \$FREESURFER_HOME."
+      for filename in "license.dat" "license.txt" ".license"
+      do
+        if [[ -f "$FREESURFER_HOME/$filename" ]]
+        then
+          echo "Trying with '$FREESURFER_HOME/$filename', specify a license with --fs_license to overwrite."
+          export FS_LICENSE="$FREESURFER_HOME/$filename"
+          break
+        fi
+      done
+      if [[ -z "$FS_LICENSE" ]]; then echo "ERROR: No license found..." ; exit 1 ; fi
+    else
+      echo "ERROR: $msg"
+      exit 1;
+    fi
   elif [[ ! -f "$FS_LICENSE" ]]
   then
     echo "ERROR: $msg, but the provided path is not a file: $FS_LICENSE."