enable config input about dcm2niix HOT 5 CLOSED

I think you would want to use the dcm2niibatch version, e.g. "dcm2niibatch run_configuration.yaml" as described here
https://github.com/neurolabusc/dcm2niix

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Thanks for the info!

A side note:
I was running into problems with the makefile not being able to find the path to yaml-cpp lib, so had to hack the paths directly. Perhaps adding a subtree of the yaml-cpp git repo to this one could make the process more user-friendly?

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@mgxd,

Yes. We need to look into making the dependencies of dcm2niibatch a bit more user friendly. Did you also have pkg-config installed? Did you install yaml-cpp through apt-get or brew, or manually? Perhaps, writing a FindYamlCpp.cmake file that also searches the local path is an option. Unfortunately, cmake doesn't come with a FindYamlCpp.cmake file already.

When I added dcm2niibatch, I tried to make the footbprint as small as possible to not distract from the main binary dcm2nii

Ben

p.s We've just put this batch version together and it still needs a few tweaks so please let us know if you run into other issues.

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@benjaminirving, yes pkg-config was already installed - the only missing component was yaml-cpp, which I installed by git cloning the repo and then building it manually.

Does dcm2niibatch use the same dicom conversion method as dcm2niix? I assumed it did.

Thanks Ben, and I'll let you know if I encounter other issues

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@mgxd, yes, the methods for dicom processing are identical. The only thing different is some wrapper code to read the yaml file and pass the inputs. But there could be some improvements in how we do that.

pkg-config will probably only be able to find yaml-cpp if installed via a package manager like apt-get or homebrew. I'll look into this.

Ben

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