[Loris-dev] BIDS - AcquisitionType

[Morales Pinzon, Alfredo]

Hi Cécile,

Thank you for the explanation. I’ll check with the team if this changes is required for our project.

Best,
Alfredo.

On Aug 17, 2021, at 9:04 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

I just verified the BIDS specification. The modality (aka acquisition type) is the last component of the file name, so in the case of the MT0 T2w, the t2w acquisition type is correct. What is stored behind the acq- string are actually acquisition parameters not the acquisition type per se.

If you really want to add the acq prefix to the scan type, you could always modify this line of code<https://secure-web.cisco.com/1_Mi0tGkwGZlsC_57j1f44QdA8RR5bpfcRJl1P5pDWTBiInJ_GWqb9syT49tK6o51AxJLJtwBNmpzBN3bQhvE_pjfHOiuYOKPeT3YUubJi_JXX731ZWY79KebVrJdBoyzREnIeb9c1T9JHLg_2TrmPxVCnrloRbAWzDJJshhsrR3Q3IJm8IjN2QbVOjsBvie5QlmMnBVBjCc1qW82vDI5bEqNVxXJ9yLNDaiAmzhZUeSHgEN_JMBHFSCU9zlB4g--byo7cedmGj5Xiri8LWMMSQ/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2F15df82251e8011b263effebbf95104737bfc97b4%2Fpython%2Flib%2Fmri.py%23L282> so that it also takes the acq prefix when looking for a scan type?

Cécile

On Mon, Aug 16, 2021 at 3:51 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LorisDev team,

I have a question regarding the AcquisitionType assigned to images imported using the BIDS functionality: how do you assign the AcquisitionType?

For some cases it looks good, but some it doesn’t match the “acq” label in BIDS:

Example of correct acquisition type:
===
        {
            "OutputType": "native",
            "Filename": "sub-BGK104001_ses-month36_run-2_T1w.nii.gz",
            "AcquisitionType": "T1w"
        }
===

Example of wrong acquisition type, in this case it should be MT0.
===
        {
            "OutputType": "native",
            "Filename": "sub-BGK104001_ses-month36_acq-MT0_run-1_T2w.nii.gz",
            "AcquisitionType": "t2w"
        },
===

Would it be possible to modify the way the acquisition types are being assigned so that it takes the “acq” label from BIDS?

Thank you for your help.

Best regards,
Alfredo.
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