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Import NIfTI/json , json format #21

Open manuegrx opened 2 months ago

manuegrx commented 2 months ago

Hi,

I would like to use mri_conv to import NIfTI/json (not organized in BIDS ).

When I export the data (via the basket), the json is copied as is and therefore does not have the same format as the others json files exported by mri_conv ( json IRMaGe). For Populse mia it is an issue but maybe it is not an issue for others uses.

As in the DictionnaryMRI_System.yml there is indications for "whereNifti", I thought it will create a json with the same format as usual (and with the tag recognised by "whereNifti") .

Emmanuelle

montigno commented 1 month ago

Hi Emmanuelle,

I will be able to look at this issue this week.

For now, mri_conv does not rebuild json when exporting from NifTi to NifTi, it only duplicates.

Where do your raw Nifti come from? Maybe I can add in the yaml dictionary another indication than 'whereNifti' (whereNiftiDicom2niix for example).

Olivier

manuegrx commented 1 month ago

Hi,

I have several cases, the raw NIfTI and JSON can come from dcm2niix or it can be also a NIfTI from a pipeline and with a json "handmade". In this last case I thought that if I used the same json tag in my json "handmade" as written for "whereNifti" (the keyName) in the DictionnaryMRI_System.yml, it could create a new json (with the json IRMaGe format)

montigno commented 1 month ago

Hi,

In the Dcm2niix json, there is a tag "ConversionSoftware", this could help me to know the origin of the conversion. In your "handmade" json, do you have the possibility to add this tag? and specify its value?

manuegrx commented 1 month ago

Yes I can add this tag !

montigno commented 1 month ago

In the Dcmi2niix json, we have "ConversionSoftware": "dcm2niix". What value do you want to set?

manuegrx commented 1 month ago

What you want ! I do not have a precise idea, I think it should be quite generic.

Quick question , why it is not possible to use the 'whereNifti' that is already in the DictionnaryMRI_System.yml ?

montigno commented 1 month ago

Hi Emmanuelle,

I pushed a new version to the dvpt branch.

Now we can export the Nifti/Json from dcm2niix. For the "handmade" ones, you need to add "ConversionSoftware: handmade" in your json.

I did some tests on some files, I think you will do more tests, you will tell me if you encounter any problems.

Olivier