Add script/instructions to convert DICOM data to BIDS

[jcohenadad]

The Stanford site needs a script with instructions to convert their data to BIDS format. I suggest using dcm2bids and add the custom JSON config file in this repository.

In terms of organization, I suggest creating a bids_conversion/ folder, with all JSON files enclosed and a README.md file with instructions.

The first step would be for @alexfoias to get in touch with the Stanford group to understand how their DICOM data are organized.

[kennethaweberii]

@andrewsm8 can you provide @alexfoias with a description of how your DICOM data are organized.

[andrewsm8]

Hello @kennethaweberii and @alexfoias,

I have the axial T2-weighted images organized as follows:

AxialDICOMs Project folder -> Each participant has a subfolder labeled using their 4-digit code -> ~30 axial DICOMs for each participant.

I can certainly organize in a different manner if necessary.

[jcohenadad]

@alexfoias is currently on vacation, coming back in September 6th, and he will contact you right away to get this done

[alexfoias]

@jcohenadad I have contacted @andrewsm8 by email for more details since we are dealing with confidential information.

[andrewsm8]

@jcohenadad I have contacted @andrewsm8 by email for more details since we are dealing with confidential information.

Hello @alexfoias, I met with @kennethaweberii and we successfully installed dcm2bids. Within a Conda environment, the following to activate that environment:

source activate dcm2bids.

We then ran the following:

python curate_bids_ucd.py -i /Users/asmith034/desktop/R03/data -o OUTPUT_PATH -c config_file_ucd.txt

It appears the script gives us the .json files and .tsv, but it is not converting the DICOM files into NIFTI. We get the following error message:

INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: macOS-11.6-x86_64-i386-64bit
INFO:dcm2bids.dcm2bids:python:version: 3.9.7 | packaged by conda-forge | (default, Sep 23 2021, 07:31:23) [Clang 11.1.0 ]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.6
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20210317
INFO:dcm2bids.dcm2bids:participant: sub-5493
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: /Users/asmith034/Desktop/dcm2bids-tutorial/config_file_ucd.txt
INFO:dcm2bids.dcm2bids:BIDS directory: /Users/asmith034/Desktop/dcm2bids-tutorial/OUTPUT_PATH
INFO:dcm2bids.utils:Running dcm2niix -b y -ba y -z y -f '%3s_%f_%p_%t' -o OUTPUT_PATH/tmp_dcm2bids/sub-5493 /Users/asmith034/desktop/R03/data/5493
Traceback (most recent call last):
File "/opt/anaconda3/envs/dcm2bids/bin/dcm2bids", line 10, in
sys.exit(main())
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2bids.py", line 291, in main
return app.run()
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2bids.py", line 120, in run
dcm2niix.run(self.forceDcm2niix)
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2niix.py", line 90, in run
self.execute()
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2niix.py", line 100, in execute
output = run_shell_command(cmd)
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/utils.py", line 113, in run_shell_command
return check_output(shlex.split(commandLine))
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/subprocess.py", line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'OUTPUT_PATH/tmp_dcm2bids/sub-5493', '/Users/asmith034/desktop/R03/data/5493']' returned non-zero exit status 2.
Traceback (most recent call last):
File "/opt/anaconda3/envs/dcm2bids/bin/dcm2bids", line 10, in
sys.exit(main())
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2bids.py", line 290, in main
app = Dcm2bids(**vars(args))
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2bids.py", line 49, in init
self.dicomDirs = dicom_dir
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2bids.py", line 90, in dicomDirs
raise FileNotFoundError(dir_not_found)
FileNotFoundError: ['/Users/asmith034/desktop/R03/data/.DS_Store']
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: macOS-11.6-x86_64-i386-64bit
INFO:dcm2bids.dcm2bids:python:version: 3.9.7 | packaged by conda-forge | (default, Sep 23 2021, 07:31:23) [Clang 11.1.0 ]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.6
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20210317
INFO:dcm2bids.dcm2bids:participant: sub-5416
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: /Users/asmith034/Desktop/dcm2bids-tutorial/config_file_ucd.txt
INFO:dcm2bids.dcm2bids:BIDS directory: /Users/asmith034/Desktop/dcm2bids-tutorial/OUTPUT_PATH
INFO:dcm2bids.utils:Running dcm2niix -b y -ba y -z y -f '%3s_%f_%p_%t' -o OUTPUT_PATH/tmp_dcm2bids/sub-5416 /Users/asmith034/desktop/R03/data/5416
Traceback (most recent call last):
File "/opt/anaconda3/envs/dcm2bids/bin/dcm2bids", line 10, in
sys.exit(main())
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2bids.py", line 291, in main
return app.run()
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2bids.py", line 120, in run
dcm2niix.run(self.forceDcm2niix)
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2niix.py", line 90, in run
self.execute()
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/dcm2niix.py", line 100, in execute
output = run_shell_command(cmd)
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/site-packages/dcm2bids/utils.py", line 113, in run_shell_command
return check_output(shlex.split(commandLine))
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/subprocess.py", line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/opt/anaconda3/envs/dcm2bids/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'OUTPUT_PATH/tmp_dcm2bids/sub-5416', '/Users/asmith034/desktop/R03/data/5416']' returned non-zero exit status 2.
[]

[alexfoias]

Hi @andrewsm8 ,

I had that type of issue in the past. Please see here: UNFmontreal/Dcm2Bids#139

I will right down a procedure on the PR so you can have all the dependencies properly configure.

Could you please let me know what OS are you using ? Thank you.

[andrewsm8]

@alexfoias, @kennethaweberii, yes I am using macOS Big Sur Version 11.6. Thank you!

[alexfoias]

Okay. Perfect. I will reach back to you with more details.

[alexfoias]

@andrewsm8 I have added some instructions on the PR. Please check them out. If you still have issues, please feel free to contact me.

[jcohenadad]

@andrewsm8 I have added some instructions on the PR. Please check them out. If you still have issues, please feel free to contact me.

@alexfoias could you please cross-reference the PR you are referring to?

[alexfoias]

Yes, I have added the link to the latest comment on the PR.

[kennethaweberii]

@jcohenadad @alexfoias We are exporting our spinal cord and lesion segmentations for our axial T2w images. Should the spinal cord segmentation contain the lesion segmentation? In other words, should the lesioned tissue be considered as part of the spinal cord? Thanks, Ken

[jcohenadad]

@jcohenadad @alexfoias We are exporting our spinal cord and lesion segmentations for our axial T2w images. Should the spinal cord segmentation contain the lesion segmentation? In other words, should the lesioned tissue be considered as part of the spinal cord? Thanks, Ken

yes