inspired - add data
#208
Comments
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I added a few commits to this branch, after running
Now, there are still some bids-validator errors, but I'm not sure what they mean, so maybe you can fix them: There are also a few warnings. If we don't care about them, we should add a |
Thank you!
Thank you! I copied the existing JSON files from the provided non-BIDS dataset. This is how this happened.
Thanks! Sure, all
This is weird! I checked the files and number of DWI volumes corresponds with the number of bval and bvec values: In other words,
This is a relevant warning-- each DWI
Might these warnings be caused by the fact that the dataset contains subjects from two centres? This is why, for example, naming is not the same ( |
Done in a new commit
It looks like this may be a bug in bids-validator. According to this forum post, it can happen when the folder contains multiple The best fix would be to open an issue and/or a PR in bids-validator, but in the meantime we can configure it to ignore this error. Or, that forum post says maybe some renaming of the files could fix the problem, but I'm not sure what the implications are.
Ah! I hadn't paid attention to the fact that there was a script to BIDSify the dataset (even though you clearly wrote so in the description). Is it a problem that I've been adding "manual" commits on top, instead of improving the script? Regardless, we should probably create these missing files with the appropriate zero values, I think.
For the author warning, I think we haven't been caring about that for our internal datasets, so I'm happy to ignore that. For the other warnings, I don't think it's because of the naming scheme. I think the files and/or parameters are genuinely different. For example, looking at just the I know we expect some of our other datasets to be heterogeneous, but do we expect the |
Agree. Could you please configure the bids-validator to ignore this? (Does it mean just to add these files to .bidsignore?)
I hope not. We have everything documented here on GitHub anyway.
Agree; I will create these files and add them in a new commit. I also found a relevant discussion about bval and bvec files for b=0 images here.
Okay!
Most of the subjects have 8 dwi files. Details$ for sub in sub*;do cd $sub/dwi;echo "$sub $(ls -1 | wc -l)";cd ../..;done
sub-torontoDCM001 8
sub-torontoDCM005 8
sub-torontoDCM006 8
sub-torontoDCM007 8
sub-torontoDCM008 8
sub-torontoDCM009 8
sub-torontoDCM010 8
sub-torontoDCM015 8
sub-torontoDCM017 8
sub-torontoDCM018 8
sub-torontoDCM019 8
sub-torontoDCM021 8
sub-torontoDCM022 8
sub-torontoDCM023 8
sub-torontoHC001 8
sub-torontoHC002 8
sub-torontoHC004 8
sub-torontoHC005 8
sub-torontoHC006 8
sub-torontoHC007 8
sub-torontoHC009 8
sub-torontoHC010 8
sub-torontoHC011 8
sub-torontoHC012 8
sub-torontoHC013 8
sub-torontoHC014 8
sub-torontoHC015 8
sub-torontoHC016 8
sub-torontoSCI003 8
sub-torontoSCI012 8
sub-zurichDCM001 8
sub-zurichDCM002 8
sub-zurichDCM003 8
sub-zurichDCM004 8
sub-zurichDCM005 8
sub-zurichDCM006 8
sub-zurichDCM007 8
sub-zurichDCM008 8
sub-zurichDCM009 8
sub-zurichDCM010 8
sub-zurichDCM011 8
sub-zurichDCM012 8
sub-zurichDCM013 8
sub-zurichDCM014 8
sub-zurichDCM015 8
sub-zurichDCM016 8
sub-zurichDCM017 8
sub-zurichDCM018 8
sub-zurichDCM019 8
sub-zurichDCM020 8
sub-zurichDCM021 8
sub-zurichDCM022 8
sub-zurichDCM023 8
sub-zurichDCM024 8
sub-zurichHC001 8
sub-zurichHC002 8
sub-zurichHC003 8
sub-zurichHC004 8
sub-zurichHC005 8
sub-zurichHC007 8
sub-zurichHC008 8
sub-zurichHC009 8
sub-zurichHC010 8
sub-zurichSCI001 7
sub-zurichSCI002 8
sub-zurichSCI003 8
sub-zurichSCI004 8
sub-zurichSCI005 8
sub-zurichSCI006 8
sub-zurichSCI007 8
sub-zurichSCI008 8
sub-zurichSCI010 8
sub-zurichSCI011 7
sub-zurichSCI012 8
sub-zurichSCI013 8
sub-zurichSCI014 4
sub-zurichSCI015 4
sub-zurichSCI016 7
sub-zurichSCI017 8I checked the subjects with <8 DWI files; and DWI files are also missing in the provided input dataset for such subjects. So I think we are fine with this. |
Done in |
Addressed in |
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I added two commits:
At this point, git-annex-get and bids-validator are happy, so I merged into master. |
Within the branch
jv/add_files, I added the BIDSisfied version of the INSPIRED dataset.Related PR.
The script I used for BIDSification is available here.
TODO after the merge of thejv/add_filesbranch:UPDATE: I can actually do these TODOs within this branch. So, @mguaypaq, please, wait with the merging.
participants.tsvderivativescreated in the context of the OHBM 2023 abstractThe text was updated successfully, but these errors were encountered: