Merge branch 'main' of https://github.com/baej3/petprep

Author: baej3

.coverage

@@ -1,5 +1,7 @@
 Alice Schiavone <[email protected]>
 Alice Schiavone <[email protected]> alice
+Anthony Galassi <[email protected]>
+Anthony Galassi <[email protected]> bendhouseart 
 Christopher J. Markiewicz <[email protected]>
 Christopher J. Markiewicz <[email protected]> <[email protected]>
 Christopher J. Markiewicz <[email protected]> <[email protected]>
@@ -15,5 +17,7 @@ NiPreps Bot <[email protected]>
 NiPreps Bot <[email protected]> nipreps-bot
 Oscar Esteban <[email protected]>
 Oscar Esteban <[email protected]> <[email protected]>
+Rami Hamati <[email protected]>
+Rami Hamati <[email protected]> ramroomh
 Ruben Dörfel <[email protected]>
 Ruben Dörfel <[email protected]> RDoerfel

.mailmap

@@ -8,8 +8,14 @@ Before every release, unlisted contributors will be invited again to add their n
 
 | **Lastname** | **Name** | **Handle** | **ORCID** | **Affiliation** |
 | --- | --- | --- | --- | --- |
+| Bilgel | Murat | @bilgelm | 0000-0001-5042-7422 | National Institute on Aging |
+| Ceballos | Eric | @eric2302 | 0000-0002-5643-1243 | Montreal Neurological Institute |
+| Dörfel | Ruben | @RDoerfel | 0000-0002-5920-5102 | Karolinska Institutet, and Neurobiology Research Unit |
 | Esteban | Oscar | @oesteban | 0000-0001-8435-6191 | School of Engineering, HES-SO University of Applied Sciences and Arts Western Switzerland, Sion, Switzerland |
+| Galassi | Anthony | @bendhouseart | 0000-0001-6550-4574 | Data Science and Sharing Team, National Institute of Mental Health, Bethesda, MD, USA |
 | Goncalves | Mathias | @mgxd | 0000-0002-7252-7771 | Department of Psychology, Stanford University, CA, USA |
+| Hamati | Rami | @ramroomh | 0000-0001-7213-9253 | Institute of Mental Health Research |
+| Jonghyun | Bae | @baej3 | 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 |
 | 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/