Rough code adding some support for manifest #18
Conversation
scanner_software_versions_pd
get from SoftwareVersions
edited at line 165:
dict_append(image03_dict, 'scanner_software_versions_pd',
metadata.get("HardcopyDeviceSoftwareVersion", ""))
to
dict_append(image03_dict, 'scanner_software_versions_pd',
metadata.get("SoftwareVersions", ""))
image_slice_thickness SliceThickness
Inserted at line 170
dict_append(image03_dict, 'image_slice_thickness',
metadata.get("SliceThickness", ""))
Edited to include image_orientation image_orientation: modified from https://stackoverflow.com/questions/34782409/understanding-dicom-image-a ttributes-to-get-axial-coronal-sagittal-cuts and rordenlab/dcm2niix#153 (comment) photomet_interpret: from DICOM/JSON field PhotometricInterpretation
Added a notes section talking about required experiment_id field
Updated for SliceThickness and PhotometricInterpretation
There was a redundant if/else confusing things. I removed it.
Also a value always has to be assigned to each element of
image03dict the conversion to a dataframe fails
I think its the id listed for collection on the NDA site.
* commit 'bd3fb46fc8c1c3bb02abe07ecb0bb4c92df23d89': add FLASH to possible scantypes # Conflicts: # bids2nda/main.py
|
I am pushing more changes to #13 to get that one usable. I guess conflicts will pile up :-/ But I am not clear from the description of this PR what manifests we are talking about? |
|
Sorry for the lack of clarity. Manifests are the NDA's way of specifying an image file and some associated non-image files along with a directory structure in which to place them. In other words, manifests are going to be the best way to represent bids data structures in NDA datasets. There is not a lot of overhead to dealing with manifests, but there is some. Would it be better for me to submit this as a PR to mtnhuck:master or just wait for that PR to be closed, rebase my branch, and resubmit? |
|
What is there beast official source to read about them more? |
|
As far as I know, this is the best documentation for the Manifest feature: https://docs.google.com/document/d/1Qo3etvKgDx1lQH37lbKik5IPuLaif9-LHEaUVIBbiz4/edit#heading=h.wng6mfab9jp2 |
|
@yarikoptic and @Shotgunosine this was early documentation for piloting the feature while it was in development. We have some detail on the NDA site, which links out to https://github.com/NDAR/manifest-data. The GitHub repo is the most recent documentation and provides some helper scripts for creating manifests. @ushnaahmad has left NDA for a new opportunity with with GeneDx. You may also be interested in feedback from @ericearl as he is about to submit all ABCD Study imaging data in BIDS format sing NDA manifests. |
|
@Shotgunosine would you be interested to come back to this PR to facelift it and finalize? I can promise to be active too. ----experiment-id was also proposed in another PR #37 by @ljchang : so it is required only for functional and not anatomicals/dwi? (in #37 it is mandatory) |
|
@yarikoptic I haven't had to interact with NDA uploading for a few years now, so my memories of all of this are pretty dim. I don't really have the bandwidth to fully re-establish context on this, but I might be able to chip in on small stuff. @obenshaindw, I know you're not and NDA anymore, but do you know anyone there who might be willing to give us some guidance on this? |
In both of these cases,
But I don't know all the cases. |
I'd suggest Greg Magdits and/or Karl Kuntzelman. But neither of them seem to be @-able. |
|
I emailed Greg and Karl and got the following helpful info from Greg:
|
|
Also, the Google Doc that @Shotgunosine linked above is dated 2018. The manifest documentation in the NDA github repo is a bit newer, but I'm not sure if it as comprehensive. |
|
@yarikoptic Did you know this was a thing? https://ndabids.readthedocs.io It's a set of tools I helped create in the DCAN Labs to upload the ABCD-BIDS Community Collection (ABCC) data to NDA collection 3165. It relies on YAML and a little JSON to map files as-is to NDA data structures and upload in batches of records. I'm happy to answer any questions or pull other people into the conversation. This was the manifest "code" used there: https://github.com/DCAN-Labs/nda-bids-upload/blob/main/records.py#L259-L281 |
No description provided.