Specifying dcm2niix version used in Nipype

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1

Dear nipype and dcm2niix experts,

I am trying to perform DICOM to NIFTI BIDS conversion using heudiconv that relies on nipype and dcm2niix. I installed heudiconv and its dependencies in a conda environement where I have several versions of dcm2niix installed. Is there a way to specify the version or path of the dcm2niix instance used to perform the conversion ?

I have tried to modify the cmd property of nipype DCM2NIIX class but it did not worked.

Best Regards
Alexandre

2

Why not just to adjust your PATH env variable and have leading folder which would point to the place with the desired version of dcm2niix binary, e.g. PATH=/my/path/to/dcm2niix-v1.0.20220720:$PATH my_nipype_script.py ?

3

Thanks @yarikoptic for your answer, your solution is working fine.

At first, I wanted to keep apart environment specification and code execution (I am using a python script to automatically generate heuristic.py file from a configuration file and run the conversion using workflow python function of heudiconv)

Have a nice day
Alexandre