Hi Chris,

Fortunately, this is me, so these DICOMS are posted publicly for my students to use. Here's the dataset:  https://osf.io/mqgzh

Since I'm running on mac, I don't have to worry about the ownership issue.

I went inside the container:

docker run -ti -v ${PWD}/out:/nifti_dir -v ${PWD}/out/dcm:/output_dir -v ${PWD}/T1_mprage_1mm_13:/original_dicom_dir  mri_reface

Then I went to the root and made sure all the bind mounts worked (they looked good)

Conversion works if I specify the NiFTI file to convert, but not if I specify just the directory containing it:

 root@0cef076d50e6:/# /usr/bin/mlrtapp/ADIR_nii2dicom nifti_dir/T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13_deFaced.nii output_dir

WARNING: Study Instance UID not found, generating new UID.
WARNING: Frame Instance UID not found, generating new UID.
Finished writing 256 dcm files to outDir: output_dir

The dcm files have tags and I can convert them to NIfTI with dcm2niix so this seems to succeed!

________

However, if I try to additionally specify the originalDicomDir, I get an error:

root@797ec2f975da:/# /usr/bin/mlrtapp/ADIR_nii2dicom nifti_dir/T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13_deFaced.nii output_dir original_dicom_dir

Traceback (most recent call last):
  File "/usr/bin/mlrtapp/ADIR_nii2dicom", line 72, in <module>
    nii2dicom(args['<nii>'], args['<outDir>'], args['<originalDicomDir>'],verbose=args.get('--verbose',False),sliceDim=int(args.get('--sliceDim')),modality_default=str(args.get('--modality')),manufacturer_default=str(args.get('--manufacturer')),photometric_default=str(args.get('--photometric')),dry_run=args.get('--dry-run',False),uid_root=str(args.get('--UID_ROOT')),seriesNUM_select=args.get('--seriesNUM_select',None),seriesUID_select=args.get('--seriesUID_select',None))
  File "/usr/bin/mlrtapp/image_handling/ADIR_nii2dicom.py", line 110, in nii2dicom
    dicom_0 = dicom.dcmread(gzip.open(dcmfiles[0],mode='rb')) if(dcmfiles[0][-3:] == '.gz') else dicom.dcmread(dcmfiles[0])
IndexError: list index out of range

If I try from outside the container, I also have less luck, even though I am only specifying the NIfTI image and the output directory, as I did inside the container:

dpat@saci 219 % docker run -ti -v ${PWD}/out:/nifti_dir -v ${PWD}/out/dcm:/output_dir mri_reface /usr/bin/mlrtapp/ADIR_nii2dicom nifti_dir/T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13_deFaced.nii output_dir

Traceback (most recent call last):
  File "/usr/bin/mlrtapp/ADIR_nii2dicom", line 72, in <module>
    nii2dicom(args['<nii>'], args['<outDir>'], args['<originalDicomDir>'],verbose=args.get('--verbose',False),sliceDim=int(args.get('--sliceDim')),modality_default=str(args.get('--modality')),manufacturer_default=str(args.get('--manufacturer')),photometric_default=str(args.get('--photometric')),dry_run=args.get('--dry-run',False),uid_root=str(args.get('--UID_ROOT')),seriesNUM_select=args.get('--seriesNUM_select',None),seriesUID_select=args.get('--seriesUID_select',None))
  File "/usr/bin/mlrtapp/image_handling/ADIR_nii2dicom.py", line 76, in nii2dicom
    nii = nib.load(niifile)
  File "/usr/local/lib/python2.7/dist-packages/nibabel/loadsave.py", line 42, in load

This is as far as I've gotten. I appreciate your time.

-Dianne