Dockerfile for PET2BIDS

[ramroomh]

I've made a Docker image for PET2BIDS.

Here is an example usage:

docker run --rm -it \ -v /path/to/dicoms:/dicoms:ro \ -v /path/to/outputdir:/out \ [container_name] dcm2niix4pet /dicoms --destination-path /out

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📚 Documentation preview 📚: https://pet2bids--359.org.readthedocs.build/en/359/

[bendhouseart]

Love it

Downloads % docker run --rm -it -v ~/Data/OpenNeuroPET-Phantoms/source/SiemensBiographPETMR-NIMH/AC_TOF:/dicoms:ro -v ~/Downloads/testoutcontainer/:/out openneuropet/pet2bids dcm2niix4pet /dicoms --destination-path /out
2025-07-14 20:20:21,882 - pypet2bids - WARNING - Unable to locate /root/.pet2bidsconfig, returning empty dictionary. (helper_functions.py:269)
2025-07-14 20:20:21,967 - pypet2bids - DEBUG - Using default dcm2niix options: -b y -w 1 -z y (dcm2niix4pet.py:411)
Downloads % ls testoutcontainer 
PET_Brain_AC_TOF_resbrain_20210504071146_3.json					PET_Brain_AC_TOF_resbrain_20210504071146_3.nii_recording-manual_blood.tsv
PET_Brain_AC_TOF_resbrain_20210504071146_3.nii_recording-manual_blood.json	PET_Brain_AC_TOF_resbrain_20210504071146_3.nii.gz
Downloads % cat testoutcontainer/PET_Brain_AC_TOF_resbrain_20210504071146_3.nii_recording-manual_blood.tsv 
time	plasma_radioactivity	metabolite_parent_fraction	whole_blood_radioactivity
16.200000000000003	32.35522376080818	0.9923034124629081	11.167945849940288
28.2	2507.1051839992842	0.9923034124629081	4027.7881549527583
42.0	30219.040354280194	0.9923034124629081	36565.981242480346
58.8	49458.13394695519	0.987721971939862	49458.13394695519
73.8	54625.12837326382	0.9827740161749722	77625.00611051863
88.8	59463.809533870204	0.9746563823000638	84130.17644682968
105.0	64473.63615111644	0.9742698880882474	88701.1586978028
118.8	62047.75316155085	0.9738833938764313	88956.94869717865
133.8	58211.4937362152	0.972213738881385	90152.19924252281
148.8	32321.7773488539	0.9631669114047967	55018.725047026935
181.2	12244.765623047355	0.9758502716844436	35607.82633071577
301.2	7804.735625363698	0.9618167202572347	26784.480310147766
619.8	5997.736143802989	0.9275766016713092	18091.20708813831
915.0	5549.337019519456	0.8742198751800287	15843.20481706456
1807.8	4852.204521810771	0.8063604240282686	12177.168344868838
2710.2000000000003	4121.738359771471	0.7734627831715212	9460.202756354014
3610.8	3449.650985611849	0.7090395480225989	7749.452902513301
4500.0	3206.781142108247	0.6824644549763034	7079.065743302966
5409.0	3442.753686495958	0.6598984771573604	5512.041195751931
Downloads % 

[bendhouseart]

Works and approved, but please update the Readme with something like the following as a last step.

Docker Usage

To build the docker file run:

docker build . -t openneuropet/pet2bids

Then mount and run your conversions on your input folders like so:

docker run --rm -it \ -v /path/to/dicoms:/dicoms:ro \ -v /path/to/outputdir:/out \ openneuropet/pet2bids dcm2niix4pet /dicoms --destination-path /out

[ramroomh]

Great, thank you.

All done!