Merge branch 'main' into rm/sentry

Author: mgxd

.coverage

@@ -19,5 +19,4 @@ Before every release, unlisted contributors will be invited again to add their n
 | Jonghyun | Bae | | 0000-0002-3987-6603 | National Institute on Aging |
 | Legarreta Gorroño | Jon Haitz | @jhlegarreta | 0000-0002-9661-1396 | Brigham and Women's Hospital, Mass General Brigham, Harvard Medical School, MA, USA |
 | Markiewicz | Christopher J. | @effigies | 0000-0002-6533-164X | Department of Psychology, Stanford University, CA, USA |
-| Murat | Bilgel | @bilgelm | 0000-0001-5042-7422 | National Institute on Aging |
 | Schiavone | Alice | @aliswh | 0009-0006-4844-2088 | Neurobiology Research Unit, Rigshospitalet, Copenhagen and Department of Computer Science, University of Copenhagen |

.maint/CONTRIBUTORS.md

@@ -203,7 +203,7 @@ ENV PATH="/opt/afni-latest:$PATH" \
 RUN useradd -m -s /bin/bash -G users petprep
 WORKDIR /home/petprep
 ENV HOME="/home/petprep" \
-    LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
+    LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH:-}"
 
 COPY --from=micromamba /bin/micromamba /bin/micromamba
 COPY --from=micromamba /opt/conda/envs/petprep /opt/conda/envs/petprep
@@ -212,7 +212,7 @@ ENV MAMBA_ROOT_PREFIX="/opt/conda"
 RUN micromamba shell init -s bash && \
     echo "micromamba activate petprep" >> $HOME/.bashrc
 ENV PATH="/opt/conda/envs/petprep/bin:$PATH" \
-    CPATH="/opt/conda/envs/petprep/include:$CPATH" \
+    CPATH="/opt/conda/envs/petprep/include:${CPATH:-}" \
     LD_LIBRARY_PATH="/opt/conda/envs/petprep/lib:$LD_LIBRARY_PATH"
 
 # Precaching atlases

Dockerfile

@@ -139,3 +139,13 @@ This was supported by the BRAIN Initiative
 grant (OpenNeuroPET, grant ID 1R24MH120004-01A1); the Novo Nordisk Foundation (OpenNeuroPET, grant ID NN20OC0063277); the Laura and John Arnold Foundation,
 the NIH (grant NBIB R01EB020740, PI: Ghosh);
 and NIMH (R24MH114705, R24MH117179, R01MH121867, PI: Poldrack)
+
+.. _FSL: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki
+.. _ANTs: http://stnava.github.io/ANTs/
+.. _FreeSurfer: https://surfer.nmr.mgh.harvard.edu/
+.. _AFNI: https://afni.nimh.nih.gov/
+.. _PETSurfer: https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer
+.. _PETPVC: https://github.com/UCL/PETPVC
+.. _kinfitr: https://github.com/mathesong/kinfitr
+.. _PMOD: https://www.pmod.com/
+.. _BIDS: https://bids.neuroimaging.io/