dcm2nii doesn't store bval bvec anywhere

[thomas.nickson]

Hey,

I'm using nipype to reconstruct some dicoms. I started doing some dti stuff and I noticed that it won't store the bval bvecs anywhere.

This is really strange because if I pull out the command that it runs and I run it separately then it works fine and will just dump the bval bvecs in the working nipype node directory that is created. It won't even put those files there if I just run it through nipype.

Any thoughts?


Thanks,

Tom

[Chris Filo Gorgolewski]

This should not have happened. Nipype does capture the bvec and bvals files generated by dcm2nii (or at least it should). Before I ask you to send over the report files and logs I just want to check something.

Is the dcm2nii a leaf node (i.e. has no outgoing connections) in your workflow? If not do you connect the bvecs and bvals outputs to any other node?

I'm asking because be default all files that are not used further down the workflow are deleted (to save space). this can be turned off in the config.

Additionally I have recently found a bug in the dcm2nii interface that can affect some conversions. You can test the fix by using this branch: https://github.com/chrisfilo/nipype/tree/fix/dcm2nii

Best,

Chris

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[thomas.nickson]

Hey sorry I was busy and then away just getting round to these now.

I just try and connect them to the sink node to save them. Does that count?

What are the options to save everything. It must be deleting them somehow because otherwise they would be saved.

Is there an easy way to pull that branch to my python distribution to test patches in this manner?

Thanks,

Tom