[Loris-dev] BIDS - AcquisitionType

Mon Oct 4 14:30:05 EDT 2021

Hi Cécile,

Thanks for answering Alfredo’s questions. I have a couple of additional questions.

  1.  In studies where the primary image upload is done in DICOM, LORIS automatically converts and links a copy of each image volume in MINC. Can it do the same thing when the primary image upload is in BIDS format?
  2.  If not, could we convert the BIDS/NIFTI files into MINC and upload them, or will this conflict with the existing NIFTI files?
  3.  Can the primary image upload be in MINC format? Up to now, we have only uploaded MINC files for secondary data (e.g. masks).
  4.  When data are uploaded as DICOM, the generated MINC files seem to have a standardized structure, STUDY_DCCID_VisitLabel_scantype_counter.mnc, (e.g. IPMSA_609372_w24_pdw_001.mnc). Is that a LORIS feature or Pisti, did you organize the input tar files with that naming structure? The BIDS NIFTI files do not have a standardized structure, which breaks downstream processing pipelines.

Thanks,

Sridar

From: Cecile Madjar <cecile.madjar at mcin.ca>
Date: Monday, October 4, 2021 at 2:03 PM
To: "Morales Pinzon, Alfredo" <AMORALESPINZON at bwh.harvard.edu>
Cc: "loris-dev at bic.mni.mcgill.ca" <loris-dev at bic.mni.mcgill.ca>, Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca>, "Sridar Narayanan, Dr." <sridar.narayanan at mcgill.ca>, "Douglas Arnold, Dr." <douglas.arnold at mcgill.ca>, "Guttmann Charles,M.D." <guttmann at bwh.harvard.edu>, István Ákos Mórocz <istvan.morocz at mcgill.ca>
Subject: Re: [Loris-dev] BIDS - AcquisitionType

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<mailto: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<mailto: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<mailto: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<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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