open-discussion > RE: Trying Docker version
May 25, 2023  10:05 PM | Dianne Patterson
RE: Trying Docker version
Dear Christopher,

Thank you so much for directing me to the correct way to download the Docker image!  For NIfTI refacing, I ran it quite successfully using your bash script on my Mac.

However, my attempt to do dicom-to-dicom refacing failed to create revised dicoms on my machine, although the message below claims the files were written to temp.  The DICOM conversion DID create the NIfTI output.


and it created an additional directory "dcm", but it is empty.

Is this a bind mount issue, or am I missing an option?

dpat@saci 219 % T1_mprage_1mm_13 out -imType T1

You provided a directory for an input, rather than a nii file. We will assume it contains DICOM for a single series. Using the -imType flag is highly recommended with this workflow.
Running dcm2niix to convert to nii
Chris Rorden's dcm2niiX version v1.0.20230411 (JP2:OpenJPEG) (JP-LS:CharLS) GCC8.4.0 x86-64 (64-bit Linux)
Found 176 DICOM file(s)
Convert 176 DICOM as /tmp/tmp.0Ck14wBMpy/T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13 (256x256x176x1)
Conversion required 1.763774 seconds (0.552646 for core code).
'/tmp/tmp.0Ck14wBMpy/T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13.nii' -> '/var/folders/34/ylkzx8hn52q2p5d_23pc90ww0000gn/T/tmp.Mf9RI3jY/outputs/T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13.nii'
Running mri_reface, version 0.3.2
By: Christopher G. Schwarz
Temp directory: /tmp/tpd3f669d5_b341_40d7_a590_73886f1cb92c
Target file: /tmp/tmp.0Ck14wBMpy/T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13.nii
Output directory: /var/folders/34/ylkzx8hn52q2p5d_23pc90ww0000gn/T/tmp.Mf9RI3jY/outputs
Target image type: T1
Template: /root/.mcrCache9.12/mri_re0/mri_reface/images/MCALT_FaceTemplate_T1.nii
Face atlas: /root/.mcrCache9.12/mri_re0/mri_reface/images/MCALT_FaceMask.nii

Calculating affine parameters to template. This will take some time.
Using face-optimized affine.
Estimating warp to template using ANTS. This will take a while.
Transforming images to input space using antsApplyTransforms
Finding face regions using the atlas
Matching intensities of warped-template to input (DBC)
Adding Rician noise to template to match noise levels in input image, with multiplier 1
Estimated noise PSF: 0
Noise in target image norm region: 6.187167 (2.791533%)
Noise in template image norm region: 2.160575 (0.974810%)
Noise to add: 5.797668 (2.615798%)
Noise in target image air: 0.440074 (16.009274%)
Noise in template image air: 0.027489 (1.000019%)
Noise to add in air: 0.439215 (210.910828%))
Replacing face
Replacing air
Saving outputs
Saved: T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13_deFaced.nii
Generating renders for QC use
Saved: T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13.png
Saved: T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13_deFaced.png
ADIR_ReFace finished in: 20.571 minutes
Traceback (most recent call last):
File "/usr/bin/mlrtapp/ADIR_nii2dicom", line 72, in
nii2dicom(args[''], args[''], args[''],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/", line 110, in nii2dicom
dicom_0 = dicom.dcmread([0],mode='rb')) if(dcmfiles[0][-3:] == '.gz') else dicom.dcmread(dcmfiles[0])
IndexError: list index out of range
DICOM file directory is empty.
De-faced DICOM was written to /var/folders/34/ylkzx8hn52q2p5d_23pc90ww0000gn/T/tmp.Mf9RI3jY/outputs/dcm. This DICOM metadata is NOT otherwise de-identified. Only de-facing was performed. If you need the meta-data de-identified also, you should run it through your preferred DICOM de-identification software.

Thank you for your time and the great project!


Threaded View

Dianne Patterson May 24, 2023
Christopher Schwarz May 30, 2023
Dianne Patterson May 31, 2023
Dianne Patterson May 29, 2023
RE: Trying Docker version
Dianne Patterson May 25, 2023
Christopher Schwarz May 26, 2023
Dianne Patterson May 28, 2023
Christopher Schwarz May 25, 2023
Christopher Schwarz May 24, 2023