dcm2nii recursively

[Michaël Bernier]

Hello folks,

I'm new to nipype, so my question might be basic..

I want to use the dcm2nii interface from nipype, but it only takes a single file in parameter. I tried to feed it a path to a folder and specify the "-r y" tag in the "arg" parameter, but it doesn't work.

So is it possible to use dcm2nii recursively, as I used to do it outside nipype, or it is not supported?

Thank you in advance for the help!

[Satrajit Ghosh]

hi michael,

you'll need to give it all the files that you would like to convert.

try the following:

from glob import glob

filenames = glob('/path/to/dcmdir/*.dcm') # assuming your file end with dcm

dcm.inputs.source_names = filenames

cheers,

satra

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[Michaël Bernier]

Thanks for the reply. However, all my files are in different subfolders and have no extension (old Siemens dicom). I will try tomorrow to get all the files recursively using grop or whatever, but I hoped for a simpler solution :P

[Ben]

Hey there - I solved this by writing an interface that consolidates all of my dicoms into one folder using hard links. Then I can just hand dcm2nii one of those files, and it takes care of everything in that directory.

Check out this gist: https://gist.github.com/beOn/6665660

You're free to use that code all you like.

[Fred Loney]

I find the Siemens DICOM file structure bothersome enough that I wrote the lndicom.py script to create links to the DICOM files in a single directory. The link file names are cleaned up to remove spaces and add a .dcm extension.

Alternatively, you can wrap the script's dicom_files method in a Nipype Function node.

This script requires that you install the pydicom Python package, which you need anyway to do anything with DICOM.

Fred