Version Release Notes
First version: 08.24.2012
Current version: 10.15.2018
- Fixed flipping in output DICOM’s, affecting MaskFace.12.27.2017.nomatlab.lin64.zip distribution.
- A Docker image supporting XNAT 1.7 container service is released. Docker image: https://hub.docker.com/r/mohanar/facemasking. Container service command: https://bitbucket.org/mohanar_radiologics/radiologics_containers
New in version 12.27.2017:
- A version that works using Matlab Runtime Environment (no Matlab license required) is released.
- Fixes to work correctly on Ubuntu machines
New in version 01.24.2014:
- Reworked the structure of the script into procedure-based
- The script now accepts multiple scans to process with the same parameters.
- The following modes of face masking are allowed by script
- based on FSL-coregistered coordinates file (generated by fsl after coregistration)
- based on supplied ROI coordinate file
- based on explicitly supplied ROI coordinates
- based on the reference scan
- each masking region requires a separate run of mask_surf_auto.m
- 3D snapshots
- tweaked brain mask application to exclude more boundary voxels
- better support of anisotropic voxels
- added ear masking
- major updates to the face masking xnat pipeline:
- new parameters:
- ref: reference scan
- use_manual_roi: signal that manual ROI will be used instead of auto-registration.
- rois: specification of manual ROI’s
- dirs: ROI normal direction (s)
- step 0: scan lists are converted to be used with xnat2loc
- step 1: xnat2loc is now used to download and process DICOM scans instead of XNATRestClient.
- new face masking script takes a list of scans, reference and ROI parameters as input.
- new parameters:
mask_face <image>[,<image>..] [options]
The first argument must list one or more MR head image files. If more than one image is specified, you must also specify one of them as reference with -r option. The reference image will be used for spatial co-registration with an atlas, and others will use the reference facial mask.
By default, the input is the DICOM directory of a single series. You can also supply images in Analyze/NIFTI (.hdr/.img pair) format by adding -a option. The output and input formats are the same.
For the complete set of options, run mask_face without parameters.
|-a||Required if you are supplying images in Analyze/NIFTI (.hdr/.img pair) format|
Method used (coating, blur, normfilter, all):
Mask threshold: Threshold is selected automatically (recommended), but can be changed with this option
|-s <grid_step>||Grid Step: Larger grid step will result in coarser looking 3D renderings, and tends to modify more voxels outside of the immediate near-surface|
Control the amount of intermediate output:
|-b||Generate the brain mask used by FSL's bet algorithm prior to face masking and use it to exclude brain voxels from modification|
Toggles the use of manual ROI coordinates
|-r <image>||Required if more than one image is being defaced. The reference image will be used for spatial co-registration with an atlas, and others will use the reference facial mask. (Use the highest quality image for your reference.)|
The algorithm main paper:
- Milchenko, M. V. & Marcus, D. (2012). Obscuring surface anatomy in volumetric imaging data. Neuroinformatics. doi: 10.1007/s12021-012-9160-3