[Loris-dev] BIDS - AcquisitionType

Cecile Madjar cecile.madjar at mcin.ca
Mon Oct 4 14:03:27 EDT 2021 

Hi Alfredo,

Indeed, you could change the AcquisitionProtoolID in the files table so
that it points to the t1g scan type.

Cécile

On Mon, Oct 4, 2021 at 1:28 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi Cécile,
>
> Thank you for the explanation, I will use this solution for a future
> dataset.
>
> Right now, I have already uploaded the datasets, and would like to change
> the scan type for some of the images. For instance I need to some T1w to
> t1g, which is a T1 with gadolinium. Can I change directly the
> AcquisitionProtocolID for the files in the database for the right one?
>
> Best,
> Alfredo.
>
> On Oct 1, 2021, at 4:51 PM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> I found the line of code that set the scan type to the BIDS suffix in
> LORIS-MRI:
> https://github.com/aces/Loris-MRI/blob/c69c89d0c64838e4a174b4a267a1406ce724878a/python/lib/mri.py#L279
> <https://secure-web.cisco.com/1UotySIw4Y2UoN0ITMqzfPkDOydrk7qYoBcSx9vos65ADL0nt4u1wQ89tO6cofPRHe7ZfZfa7BS5RTZ14d2w6mn-7-caoug2oyTPjfsq4w43Hkk45pzAq7isYEmrQ1JsG0bzYc6wldk7P4oiYp6L1g8R5nMjhdKe05hfwTTZ5E-ZRZJDx3n8OB8hRhx_W1sdTDxTfzk_7wurHqkj7xdiRJxH3MQO0aMq_Por4w9xLwvYqH_iwLF4BGeCVIaXPbnjQrCMIDULeStGAwClTF4jFug/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fc69c89d0c64838e4a174b4a267a1406ce724878a%2Fpython%2Flib%2Fmri.py%23L279>
>
>
> In line 278, nifti_file.get_entities() will return T1w for files that are
> named according to BIDS
> sub-xxx_ses-xxx_<various_parameters>_<suffix>.nii.gz. In your case, the
> suffix is T1w, which is what is being used to determine a scan type.
>
> I don't know what t1c or t1g refers to but I am guessing that some of the
> information is available elsewhere in the filename or the JSON file
> to determine what is what? In which case, you could modify line 279 so that
> the scan_type is determined based on the criteria you wish to use.
>
> Does that make sense?
>
> Hope this helps,
>
> Cécile
>
> On Thu, Sep 30, 2021 at 10:57 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi Cécile,
>>
>> We would like to improve the acquisition type assigned in LORIS for some
>> images that we had uploaded into LORIS for two BIDS datasets. For instance
>> we would like to change some “T1w" to “t1c" or “t1g", depending on some
>> parameters. Is it possible? could you guide me on how can I do this change
>> in LORIS? I’m happy to write some sql scripts if needed.
>>
>> Best,
>> Alfredo.
>>
>> On Aug 17, 2021, at 9:04 AM, Cecile Madjar <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> 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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