Hi there:

New user of dcm2niix here. I installed MRIcroGL, running dcm2niix from the command line on Mac (El Cap). Am using to convert data acquired on a Philips 3T -- 3D structural and resting state. Here is the syntax I used:

dcm2niix -o "Users/username/blah/moreblah/NIFTI_subdirectory" -z n /Users/username/blah/moreblah/DICOM_filename_for_individual_image

The conversion ran, but I experienced the following:

1. Couldn't find my output directory
2. Converted all my dicoms, instead of a single one
3. Gave me individual volumes for the resting state

I am wondering what I'm doing wrong with specifying the output directory, how to specify a single file if desired, and if there is an option to concatenate the volumes for the resting state in to 4D during conversion or if I need to do 3D to 4D file conversion as a separate step.

Thanks very much,

Nina de Lacy