[ENH] Update pet2bids version and fix 4D singleton dimension issue

Author: Dan Levitas

handler/Dockerfile

@@ -10,7 +10,7 @@ RUN apt update && \
 RUN apt install -y parallel python3 python3-pip tree curl unzip git jq python libgl-dev python-numpy
 
 RUN pip3 install numpy==1.23.0 nibabel==4.0.0 pandas==1.0.1 matplotlib pyyaml==5.4.1 pydicom==2.3.1 natsort pydeface && \
-    pip3 install quickshear pypet2bids==1.3.2 mne mne-bids
+    pip3 install quickshear pypet2bids==1.3.5 mne mne-bids
 
 RUN apt-get install -y build-essential pkg-config cmake git pigz rename zstd libopenjp2-7 libgdcm-tools wget libopenblas-dev && \
     apt-get clean -y && apt-get autoclean -y && apt-get autoremove -y

handler/ezBIDS_core/createThumbnailsMovies.py

@@ -65,7 +65,13 @@ def create_thumbnail(img_file, image):
     """
 
     if image.ndim == 4:
-        object_img_array = image.dataobj[..., 1]
+        try:
+            object_img_array = image.dataobj[..., 1]
+        except:
+            # weird issue where an improper singleton 4D dimension is added for otherwise 3D data (see with PET)
+            image = nib.funcs.squeeze_image(image)
+            object_img_array = image.dataobj[:]
+            image.to_filename(img_file)
     else:
         object_img_array = image.dataobj[:]