Uses Chris Rorden's dcm2niix to convert DICOM files to NIfTI. Defaces and refaces with AFNI.
196
Built on the latest version of Ubuntu.
Converts DICOMs to NIfTI format via Roden's dcm2niix.
De/Refacing of T1-weighted images via AFNI's @afni_refacer_run.
Usage:
docker run \
-v </path/to/dcms>:/dicom \
-v </path/to/dset>:/nifti \
nmuncy/dcm2niix \
-f <file_str>
Required Arguments:
-v </path/to/dcms>:/dicom = absolute path to localhost DICOM directory
-v </path/to/dset>:/nifti = absolute path to localhost dset directory
-f = output file string sans extension
Optional Arguments:
-h = print help
-d <y/n> = deface yes/no
requires: -f <foo>_T1w
-r <y/n> = reface yes/no
requires: -f <foo>_T1w
Example Usage:
docker run \
-v /home/project/sourcedata/dicom/folder:/dicom \
-v /home/project/dset/sub-1234/ses-S1/anat:/nifti \
nmuncy/dcm2niix \
-f sub-1234_ses-S1_T1w \
-d y
Planned updates (as of 9/29/21) are to add: defacing, more BIDS compatibility, and ability to convert entire projects. We will see ...
Update 10/8/21: Added defacing.
Update 10/16/21: Added entrypoint, refacing.
Content type
Image
Digest
Size
647.3 MB
Last updated
almost 5 years ago
docker pull nmuncy/dcm2niix