NITRC mri_reface Forum: open-discussion

RE: Trying Docker version

Christopher Schwarz — Fri, 17 Nov 2023 22:45:51 GMT

Originally posted by Adam Raikes:
<blockquote>
I haven't seen any resolution to this issue, but wanted to give my experience.
I created a Singularity container from the current Docker image for use with the system I have access to. Binding the updated ADIR_nii2dicom.py as /usr/bin/mlrtapp/image_handling/ADIR_nii2dicom.py solved this problem for us.
</blockquote>
Adam,
I'm sorry you had to do that. I was waiting for confirmation from Dianne and largely forgot about this.
Today I released a new version 0.3.3 that includes this fix (and some other unrelated ones).
Thanks,
Chris

RE: Trying Docker version

Adam Raikes — Thu, 02 Nov 2023 18:44:24 GMT

I haven't seen any resolution to this issue, but wanted to give my experience.
I created a Singularity container from the current Docker image for use with the system I have access to. Binding the updated ADIR_nii2dicom.py as /usr/bin/mlrtapp/image_handling/ADIR_nii2dicom.py solved this problem for us.

RE: Trying Docker version

Christopher Schwarz — Tue, 13 Jun 2023 0:30:34 GMT

Dianne,
Thanks for posting the steps you followed. I followed your steps to create the updated image and I called it mri_reface2, as you did. I then exited and went into mri_reface2 in a new terminal and verified that the updated copy of ADIR_nii2dicom.py was still there.
$ docker run -ti mri_reface2 root@55793afdac4c:/usr/bin/mlrtapp/image_handling# grep xml ADIR_nii2dicom.py              dcmfiles_temp = [i for i in dcmfiles_temp if not re.search(r'\.xml$', i) ]
The above grep result matches the code I added newly in the revision I attached previously. 
I created a new run_mri_reface_docker.sh  $ cp run_mri_reface_docker.sh run_mri_reface2_docker.sh
Which I then edited to replace mri_reface with mri_reface2 in BOTH docker lines: 96 docker run -ti --mount type=bind,src\=$tmpdir,target=$tmpdir mri_reface2 run_mri_reface.sh $input $output_tmp ${input_array[@]:2 } 97  98 docker run -ti --mount type=bind,src=$tmpdir,target=$tmpdir mri_reface2 chmod =777 -R $tmpdi
From there I ran it two ways. One was using run_mri_reface2_docker.sh:
$ ./run_mri_reface2_docker.sh dcm_t1 outExternal -imType T1
[...] ADIR_ReFace finished in: 17.9749 minutes Finished writing 176 dcm files to outDir: /tmp/tmp.A1n3Oz3nih/outputs/dcm Including custom code sequence: code: "replace_recognizable" meaning: "Replace face, ears, and artifacts in air" designator: "mri_reface" version: "0.3.2" Finished. De-faced DICOM was written to /tmp/tmp.A1n3Oz3nih/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.
When it completed, I opened outExternal/dcm and the files are present and successful.
I also tried running the whole thing inside docker, rather than using run_mri_reface2_docker.sh
$ chmod a+wrX . $ docker run -ti --mount type=bind,src=${PWD},target=/host mri_reface2 root@23aadd07062d:/usr/bin/mlrtapp/image_handling# cd /host root@23aadd07062d:/host# run_mri_reface.sh dcm_t1 out2 -imType T1
[...] ADIR_ReFace finished in: 17.8532 minutes Finished writing 176 dcm files to outDir: out2/dcm Including custom code sequence: code: "replace_recognizable" meaning: "Replace face, ears, and artifacts in air" designator: "mri_reface" version: "0.3.2" Finished. De-faced DICOM was written to out2/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. root@23aadd07062d:/host# exit
Then I checked out2/dcm. The dcm files are present and valid.
I tried again using your dicom directory name, just in case that had something to do with it:
$ ./run_mri_reface2_docker.sh T1_mprage_1mm_13/ out -imType T1
And that was also successful. 
From here, I was at a bit of a loss. My best guess was that there's a mistake in one of the steps you didn't show me. Maybe you could verify that your mri_reface2 image has the updated code (via the above grep example), and you could verify that your run_mri_reface2_docker.sh replaced 'mri_reface' in BOTH 'docker' commands with 'mri_reface2'? 
Toward that hypothesis, I looked back at the start of your pdf and I think you may not have replaced the correct file/path.  /usr/bin/mlrtapp has ADIR_nii2dicom, a program. It also has a subdirectory called image_handling. Inside image_handling is ADIR_nii2dicom.py. I intended for you to replace /usr/bin/mlrtapp/image_handling/ADIR_nii2dicom.py, NOT /usr/bin/mlrtapp/ADIR_nii2dicom, but it looks like you replaced ADIR_nii2dicom. I surprised that didn't up with a new error message when you tried to run it that way, but otherwise I think this explains why it's now working for me, but not you. 
Can you please try starting again from the original mri_reface image and copy the new ADIR_nii2dicom.py into image_handling, this time? From there, I hope it will work for you. Please let me know. Sorry my original instructions weren't clear enough about which file to replace. 
Thanks, Chris

RE: Trying Docker version

Dianne Patterson — Fri, 09 Jun 2023 20:10:57 GMT

The dcm directory is empty again. I'm attaching a pdf that details my steps for testing.
My revised container works fine on NIfTI input, but continues to refuse to generate the revised DICOM files.

RE: Trying Docker version

Christopher Schwarz — Wed, 07 Jun 2023 15:39:56 GMT

Dianne,
I think I found the issue. Could you please try swapping in the attached copy of ADIR_nii2dicom.py for the one in mri_reface/ADIR_nii2dicom/ADIR_nii2dicom and see if that solves it for you? If it does, we can make this change in the next version. 
 Thanks,
Chris

RE: Trying Docker version

Dianne Patterson — Tue, 06 Jun 2023 20:31:52 GMT

<div class="elementToProof ContentPasted1">Is this the issue?</div>
<div class="elementToProof ContentPasted1"> </div>
<div class="elementToProof ContentPasted1"><a id="LPlnk972631" href="https://github.com/nipy/heudiconv/issues/648">https://github.com/nipy/heudiconv/issues/648</a></div>
<div class="elementToProof">
<div> </div>
<div id="Signature">
<div>
<div>-Dianne</div>
</div>
</div>
</div>

RE: Trying Docker version

Christopher Schwarz — Tue, 06 Jun 2023 19:06:22 GMT

Dianne,
I was able to download your dicom and reproduce your error. I get the same error when I simply run dcm2niix on the dicom, then ADIR_nii2dicom on the nii with the original dicom. So, the error isn't in the de-facing at all but just in converting from dicom->nii and nii->dicom with these particular inputs. We'll debug from here and get back to you soon. 
Chris
 
$ dcm2niix -o dcm2niix ./MRIS/dicom/219/itbs/T1_mprage_1mm_13
Chris Rorden's dcm2niiX version v1.0.20221013  (JP2:OpenJPEG) GCC4.8.5 x86-64 (64-bit Linux) Found 176 DICOM file(s) Convert 176 DICOM as dcm2niix/T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13a (256x256x176x1) Conversion required 1.046187 seconds (0.340000 for core code).
$ ADIR_nii2dicom dcm2niix/T1_mprage_1mm_13_T1_mprage_1mm_20180706110327_13.nii dcm2niix/nii2dicom ./MRIS/dicom/219/itbs/T1_mprage_1mm_13 Traceback (most recent call last):   File "/bin/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 "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

RE: Trying Docker version

Dianne Patterson — Wed, 31 May 2023 2:53:13 GMT

Thank you for developing this nice tool...and for being willing to look into it.  I hope you have a great holiday.

RE: Jittery Dicoms

Christopher Schwarz — Tue, 30 May 2023 23:39:54 GMT

That sounds interesting! Do you have a way to de-identify and send the dicoms for us to take a look at? I'm on holiday this week but could take a look next week, if you're able to send them. Otherwise, all I can say is we haven't seen that or heard of anything similar, before. ADIR_nii2dicom has its source code provided, so if you're comfortable with code you could try to take a look as well. We've tried to make it as robust as we can, but there's a seemingly infinite number of unusual dicom quirks in the world. If you know of a different nii2dicom converter, that'd work too, but I'm also not aware of a robust alternative that attempts to preserve the unrelated tags, as ours does.
Chris Schwarz

RE: Trying Docker version

Christopher Schwarz — Tue, 30 May 2023 23:33:58 GMT

Dianne,
Thanks for posting the DICOMs. I'm on holiday this week, but I can download them and take a look when I return next week. I will get back to you. Sorry for the trouble.
Chris Schwarz