That’s weird, since I filter out those files with:
# Skip radiology reports, as they have a very limited DICOM header
if get_dicomfield('CodeMeaning', dicomfile) == 'Radiology Report':
LOGGER.info(f"Skipping radiology report '{dicomfile}'")
continue
I’ve based this on:
I have checked the radiology reports and they all have the dicom tag (0008,0104) CodeMeaning with value ‘Radiology Report’.
Is this not true? Or are there multiple CodeMeaning fields in your report file?
Ah, forgive my error.
(0008,0104) CodeMeaning with the value Radiology Report belongs to the tag ConceptNameCodeSequence which is empty. There are actually multiple CodeMeaning tags across the dicom metadata, which I had not realised.
However, I think I’ve found a dicom tag that is common to all of the report files which also has a value in it. This is (0008,0060) ‘Modality’ which has the value ‘SR’ (standing for Structured Report document - clinical report). So I think this should be able to pick up the report files?
Can you perhaps open the bidseditor and go to the [Data browser] tab, navigate to your input data, and double click on a report file? Can you share a screenshot of that? (I presume there is no personal info in there)
p.s. You can do this everywhere in the GUI, double-click on filenames, but your report file is missing from the representative samples, hence the data browser
Ok, I’m filtering out the SR files now, same recipe as before:
source bidscoin_dev/bin/activate # If needed
pip install --force-reinstall --no-deps "git+https://github.com/Donders-Institute/bidscoin"
bidsmapper sourcedata BIDS_new -s -n 'patient-' -m '*'
bidscoiner sourcedata BIDS_new
Dear Marcel, the recipe works to a tee. I have tried it on another patient’s data as well. I can’t thank you enough for your help with this!
The only warnings now are these multiple warnings: WARNING | The referenced SOP Instance for the directory record at offset 3773042 does not exist: /private/var/folders/d9/lz2pjlr50ygdpn7ddzp2fbc40000gp/T/tmp5hggm9pt/Users/ … sourcedata/patient-01/DICOM/0000AC37/AA740734/AAB9BE77/00007A3B/FFA7A389
If I run the bidseditor on the data again, I can’t change the data-type but I have found your troubleshooting section Troubleshooting — BIDScoin 4.5.0 documentation. Out of interest, is the SOP warning above related to the data type issue?
Thank you again.
Good to hear. If BIDScoin needs to reorganize the data (for passing it to e.g. dcm2niix), it is doing so in a tmp-dir. After reading the attributes from the data in the tmp-dir it is readily deleted, which makes that you can’t re-read new attributes when editing the datatype. As you have seen in the troubleshooting guide, to make this possible, you can use bidsmapper’s -s option to store the representative samples (in bidsfolder/code/bidscoin/provenance) so that they can be re-accessed later (when editing the datatype). The reason this is not the default is that I don’t want users to unknowingly store raw (privacy-sensitive) data in the bids-folder.
This warning means that your DICOMDIR file contains a reference to a DICOM object that does not actually exist in your dataset. Essentially, there is a mismatch between what the DICOMDIR expects and what is present, e.g. due to missing or corrupted DICOM files. To investigate this in more detail it could be useful if at the start you set:
export BIDSCOIN_DEBUG=TRUE
Out of interest, is the SOP warning above related to the data type issue?
I wouldn’t expect that
Do you perhaps have any news on this? I’m asking because I’m about to publish a new bidscoin release and would like to include a fix for this if I can…
Do you know what kind of file it is? (sourcedata/patient-01/DICOM/0000AC37/AA740734/AAB9BE77/00007A3B/FFA7A389)
Edit: It seems to be one of your report files. Did you delete them? Anyhow, I think you can ignore the warning, and that I will go ahead with the new release.
Hi Marcel, FFA7A389 is a TextEdit.app Document (2kb) and, you’re correct that it is one of the report files. I hadn’t deleted the report files when I encountered the WARNING SOP.
However, the SOP WARNING has now disappeared after I ran the code afresh, so am not sure what the reason for it was! No bidscoin warnings or errors now.
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