neuroimaging-rg / bids_conversion Goto Github PK

In the wiki description, my subject name has several underscores - I think this is NOT BIDS compliant, need to check this. Using -b option might strip out _ from subject names for you, but has produced other issue - see issue on this page

I think there are 3 small problems with the docker run commands on the wiki:

1. "-c dm2niix" should probably be "-c dcm2niix"
2. On 2 occasions there is a white space missing before the -o parameter: "...niix-o /data/output"
3. Throughout the wiki page you use PQC_ADPRC_20170925 as dicom folder, except for the very last docker run command where it's ADPRC_0080_F0. This should probably be consistent.

You can use -b option before the -o for output for bids to make sure all bids required meta data are there, as a but when I it didn't do multiple image file conversions - just one! either one worked though depending on which commented out. If I didn't use -b then both files were converted as expected - don't use -b for now until work this out

I’ve not checked the content of the json files – assuming they have been generated as they should be, but as start analysing data from each image type it should be clear if they are right.

if you use -b and --minmeta option for the conversion (see wiki page for e.g.) then -b flag generates a json file with BIDS keys, and --minmeta flag restricts the json file to ONLY BIDS keys. I've had a quick look at this and e.g. the func data json file is huge if you just use -b option, but with minmeta is a lot smaller but presumably contains all the information you need.

From the main heuidiconv BIDS page "Without --minmeta, the json file and the associated Nifti file contains DICOM metadata extracted using dicomstack. "

the BIDS convention for perfusion has not be finalised yet see "useful links" on git hub code tab for asl working doc
e.g. they have not decided if asl should go in func or own folder I have made a asl folder, rather than put it in func

also the BIDS convention for SWI has not been finalised yet (again see useful links for swi working group
e.g. in main BIDS specification says SWI is anat but in working doc suggests swi folder as you can get many files for swi and QSM so I have created separate folder too for swi