JSON tag when using BIDS

[manuegrx]

Hi,

I would like to add some tags available in the BIDS JSON in the mri_conv JSON. I think that they need to be add in the DictionnaryMRI_System.yml but for some it will be necessary to add some calculation in the code.

• Slice Gap : already in the DictionnaryMRI_System.yml but not for BIDS. We can use the tag SpacingBetweenSlices and SliceThickness in the JSON BIDS and compute Sloce gap : SpacingBetweenSlices - SliceThickness

• Acquisition duration: not yet in the DictionnaryMRI_System.yml. We can use the tag AcquisitionDuration in the JSON BIDS

I also have some questions about Protocole Name and Sequence Name tag.
In the DictionnaryMRI_System.ym, the BIDS JSON tag ProtocoleName and SequenceName are correctly used but in the final mri_conv JSON it is the name of the original file that is is used (for example sequencename = sub-003_ses-01_T1w and procotolname = anat). Is there a reason ? It is possible to use the BIDS JSON tag instead?
For Sequence Name, we should used the JSON BIDS tag "PulseSequenceName"

Here is a example of a BIDS JSON with the available tag :
sub-003_ses-01_T1w.json

And the current mri_conv JSON:
sub-003---0-anat-sub-003_ses-01_T1w-153355_910000.json

[manuegrx]

As protocol name and sequence name are also used in the final name of the mri_conv file maybe it is better to have a plan if ProtocolName and PulseSequenceName tags are not available in the BIDS JSON and in this case use the name of the BIDS file.

[manuegrx]

Others questions / modifications to do:

• Software versions: currently I the mri_conv JSON there is a tag SoftwareVersions but I do not know where it came from because it is not the good version. Is it possible to add in the DictionnaryMRI_System.yml "Software Versions" and for BIDS used the tag SoftwareVersions ?

• ManufacturersModelName: not yet in the DictionnaryMRI_System.yml. We can use the tag ManufacturersModelName in the JSON BIDS (there is already the tag Manufacturer, it seems to com from Nifti header, if needed we can also used the tag Manufacturer in JSON BIDS)

• Institution ( or InstitutionName): not yet in the DictionnaryMRI_System.yml. We can used a combination from the JSON BIDS tag InstitutionName and InstitutionDepartmentName (if available)

@montigno let me know if something is not clear enough and how I can help !

[montigno]

Hi Emmanuelle,

I made the changes, I don't guarantee that everything has been fixed, I don't have much BIDS data with complete JSON.

Can you do the tests on your side?
And don't hesitate to inform me if problems remain.

Thanks!
See you soon.

Olivier

[manuegrx]

Hi,

Thank you, it seems to work well !

• Acquisition duration: ok
• Slice Gap : ok
• Institution: ok
• Software versions:: ok
• ManufacturersModelName (named manufacturer's Model) : ok
• SequenceName: ok

Regarding the data name it is also good. Note that we therefore lose the BIDS name information (for example the session number and for fMRI the task name). It could be useful to keep theses information somewhere, I let you know if I have an idea about it

[manuegrx]

Hi @montigno ,

I modified the DictionnayMRI_System.yml to add some tag:

• add Acquisition Duration for PAR REC (using Scan Duration)
• add Acquisition Number for BIDS and PAR REC

Please find here my proposition: DictionaryMRI_System.zip

Also, I think I misunderstood part of the DictionnayMRI_System.yml.
I do not understand why some information are not in the json created by mri_conv.
For example 'Number Of Slice' or 'Scan Resolution'. In the DictionnayMRI_System.yml modified above I tried to add a tagJson (json: {tagJson: ScanResolution, type: ~, format: ~, units: ~}) but it is not working. What I am missing ?

[manuegrx]

Little update for my proposition for the dictionary:
DictionaryMRI_System.zip

[montigno]

Hi @manuegrx,

Here is the modified dictionary, I did not take the time to test it thoroughly, but you can already do a test on your side.

You will tell me if it is good for you.

DictionaryMRI_System.zip

Thanks !

Olivier

[manuegrx]

Thanks ! It is working with this version :
DictionaryMRI_System.zip (little modification with SeriesNumber instead of SerieNumber)

[manuegrx]

I noticed that, for the same data imported in BIDS or imported in PAR/REC, there are differences in the order of the dataset dimension (and so in Scan resolution) and voxel size.

I think it comes from the way to keep the info in the NIfTI header.

For data in BIDS (here obtain from DICOM data) :
header_nifti_bids_dicom.txt

dim             : [  3 160 512 512   1   1   1   1]
pixdim        : [1.         0.99999994 0.49999997 0.5       0.         0.      0.         0.        ]

And so in the mri_conv json:
"Dataset dimensions (Count, X,Y,Z,T...)" : [[3],[160],[512],[512]]
"Grid spacings (X,Y,Z,T,...)": [[0.99999994],[0.49999997],[0.5]]
"Scan resolution" : [[160],[512]]

For PAR/REC data :
header_nifti_parrec.txt

dim             : [  3 512 512 160   1   1   1   1]
pixdim        : [-1.        0.5       0.5       1.        0.009904  0.        0.  0.      ]

And so in the mri_conv json:

"Dataset dimensions (Count, X,Y,Z,T...)" :[[3],[512],[512],[160]]
"Grid spacings (X,Y,Z,T,...)": [[0.5],[0.5],[1.0]]
"Scan resolution" : [[512],[512]] 

I am really not an expert in NIfTI Header but I think that it is necessary to take into account the -1 or 1 in the header pixdim value if we want to have the same order (Count, X,Y,Z,T.) .
@montigno if needed we can discuss about it during a meeting

[montigno]

Hi Emmanuelle,

I had to reinstall my PC, and reinstall everything.
Sorry for the inconvenience!

Your Bids data was converted with which application?

You can come see me and talk about all this.