conversion of single DICOM images

[efunn]

I currently use the original dcm2nii in a real-time fMRI workflow using FSL tools. Our Siemens scanner dumps DICOMs into some_folder, so I set a watch on some_folder and call dcm2nii -v n some_folder/image.dcm for each image that appears, which gives me a NIFTI that I can use FSL on.

I'm interested in using dcm2niix because of the speed increase on Siemens DICOMs. However, single image processing does not appear to be available any more.

My current solution is:

• detect path/to/unique_image.dcm appearing
• create path/to/unique_image_folder
• copy path/to/unique_image.dcm to path/to/unique_image_folder
• call dcm2niix -o path/to -f unique_image path/to/unique_image_folder
• remove path/to/unique_image_folder
• resulting in path/to/unique_image.nii and no extra folders in path/to/

I'm wondering if the option to convert single images by calling dcm2nii --some-argument path/to/single/image.dcm still exists in dcm2niix but I'm missing how to pass the argument. If not, is there any future plan to re-implement this feature?

[neurolabusc]

Hello-
I have added this feature to the 27Aug2015 release. You can either compile your own copy or use a precompiled version (in the 'osx_binary' and 'linux_binary' folders. To convert single files you would use the '-s Y' switch, so "./dcm2niix -s Y /test/myDICOM.dcm". While this software might be a touch faster than other tools for single files, the real performance benefits are seen when converting large numbers of files. With a single file disk access is probably the limiting factor. If speed is important avoid saving data in a compressed format (.nii.gz) as that has a big overhead.

[efunn]

Tested the precompiled Linux version and the '-s Y' switch works as expected. Thank you!