From cecile.madjar at mcin.ca  Fri Oct  1 16:51:38 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Fri, 1 Oct 2021 16:51:38 -0400
Subject: [Loris-dev] BIDS - AcquisitionType
In-Reply-To: <1431DEE0-4FC7-4B06-8EB5-BEDEF0A0E19B@bwh.harvard.edu>
References: <EC983D83-651E-4A10-B650-A25961C117D7@bwh.harvard.edu>
 <CAMkiY3dSF___LcDQj=fGua9wr9QgCUsmDKb6C6pBQkSQ-cbUEw@mail.gmail.com>
 <1431DEE0-4FC7-4B06-8EB5-BEDEF0A0E19B@bwh.harvard.edu>
Message-ID: <CAMkiY3chweMnEt58ntpCXyBgF0MLx5rf9-MHwRSGR0s+coHBtA@mail.gmail.com>

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


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,

C?cile

On Thu, Sep 30, 2021 at 10:57 AM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> 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?
>
> C?cile
>
> 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.
>> The information in this e-mail is intended only for the person to whom it
>> is addressed. If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Mass General
>> Brigham Compliance HelpLine at
>> http://www.massgeneralbrigham.org/complianceline
>> <http://secure-web.cisco.com/1ig3dr6i1WdAs8_-Q_MeK7GXwa0dgT1TgKI1JS7MC0k4yUeF62G6kVevDIHZj5n8tYT0kmV7nj6Fy6sEMEe-xDkf6WhZtm0M-v0uUlyhiKd_DcQ1aSPrfn2jxfJIreAitqwR42XMZb84w7G5WECzE46VWrQ3SZQgrrNHlOq19WKP-mKl5SKE-kGJwNUp4d3l-NeVnWGOTeEoLAx7yXW4HO4FcWICnHaw7zpvritbMeXJqEIaabeQmg8ZEyf_niv71lNvwche53TaBWI6any_S-g/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>> . If the e-mail was sent to you in error but does not contain patient
>> information, please contact the sender and properly dispose of the e-mail.
>>
>> Please note that this e-mail is not secure (encrypted).  If you do not
>> wish to continue communication over unencrypted e-mail, please notify the
>> sender of this message immediately.  Continuing to send or respond to
>> e-mail after receiving this message means you understand and accept this
>> risk and wish to continue to communicate over unencrypted e-mail.
>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>> <https://secure-web.cisco.com/1d3CFTBToT4j_It30C0sMIZMcTjPqg9RYBFR977oo5ohdasD5Q6U_0ZthyISkUY7Scl8QHwLUGl1JPlpSq6nGt24dMn4qVx8wLxa2UEgaCQgBVAFsdSgusVbLZfj66xn8uFJW_6Qn157m_S9eVZtPrTxUxdhnqC-Yle4xue7mwU5VhzucMFWdxp7uxzLYfwjG35JojFFEy8Aa2x9j2hSO3E-NPuUnrYeqQtR4GFLMRpTbp_8xv4S_0T1hH6fYlqR6JyiOCvcB7AV9LbjIr5GAkQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
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From AMORALESPINZON at BWH.HARVARD.EDU  Mon Oct  4 13:28:43 2021
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Mon, 4 Oct 2021 17:28:43 +0000
Subject: [Loris-dev] BIDS - AcquisitionType
In-Reply-To: <CAMkiY3chweMnEt58ntpCXyBgF0MLx5rf9-MHwRSGR0s+coHBtA@mail.gmail.com>
References: <EC983D83-651E-4A10-B650-A25961C117D7@bwh.harvard.edu>
 <CAMkiY3dSF___LcDQj=fGua9wr9QgCUsmDKb6C6pBQkSQ-cbUEw@mail.gmail.com>
 <1431DEE0-4FC7-4B06-8EB5-BEDEF0A0E19B@bwh.harvard.edu>
 <CAMkiY3chweMnEt58ntpCXyBgF0MLx5rf9-MHwRSGR0s+coHBtA@mail.gmail.com>
Message-ID: <32C3B4E3-E9A8-409C-8B6D-EF35E2794DB3@bwh.harvard.edu>

Hi C?cile,

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,

C?cile

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 C?cile,

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?

C?cile

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.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1ig3dr6i1WdAs8_-Q_MeK7GXwa0dgT1TgKI1JS7MC0k4yUeF62G6kVevDIHZj5n8tYT0kmV7nj6Fy6sEMEe-xDkf6WhZtm0M-v0uUlyhiKd_DcQ1aSPrfn2jxfJIreAitqwR42XMZb84w7G5WECzE46VWrQ3SZQgrrNHlOq19WKP-mKl5SKE-kGJwNUp4d3l-NeVnWGOTeEoLAx7yXW4HO4FcWICnHaw7zpvritbMeXJqEIaabeQmg8ZEyf_niv71lNvwche53TaBWI6any_S-g/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
_______________________________________________
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Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev<https://secure-web.cisco.com/1d3CFTBToT4j_It30C0sMIZMcTjPqg9RYBFR977oo5ohdasD5Q6U_0ZthyISkUY7Scl8QHwLUGl1JPlpSq6nGt24dMn4qVx8wLxa2UEgaCQgBVAFsdSgusVbLZfj66xn8uFJW_6Qn157m_S9eVZtPrTxUxdhnqC-Yle4xue7mwU5VhzucMFWdxp7uxzLYfwjG35JojFFEy8Aa2x9j2hSO3E-NPuUnrYeqQtR4GFLMRpTbp_8xv4S_0T1hH6fYlqR6JyiOCvcB7AV9LbjIr5GAkQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev>

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1vNmj03p92XKeNCHdbzJ-j02hi9iHbmDxay9AX247pJJJvtYwtIZyiBHqc3DUdFuSQn-nLRXFZ7dK9HaISl9ToR42zIgDmGv42q0HWNyO2XbXVYuBO2blnxwrBHKNPEKpJXf6YZ5d86OueTBOIiPRNj-any8ibCsVdxK7Sju1vNDuN1iGp5AHOyUP_7nkK_UmAKzldlMZf9wxrrGxNW1bCF5SBeMzRLWc22DUtkJj__QzI9J1VVoJEscG6fZqitTlJgnLwTgWQRQLokaxkFBUxw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
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From cecile.madjar at mcin.ca  Mon Oct  4 14:03:27 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 4 Oct 2021 14:03:27 -0400
Subject: [Loris-dev] BIDS - AcquisitionType
In-Reply-To: <32C3B4E3-E9A8-409C-8B6D-EF35E2794DB3@bwh.harvard.edu>
References: <EC983D83-651E-4A10-B650-A25961C117D7@bwh.harvard.edu>
 <CAMkiY3dSF___LcDQj=fGua9wr9QgCUsmDKb6C6pBQkSQ-cbUEw@mail.gmail.com>
 <1431DEE0-4FC7-4B06-8EB5-BEDEF0A0E19B@bwh.harvard.edu>
 <CAMkiY3chweMnEt58ntpCXyBgF0MLx5rf9-MHwRSGR0s+coHBtA@mail.gmail.com>
 <32C3B4E3-E9A8-409C-8B6D-EF35E2794DB3@bwh.harvard.edu>
Message-ID: <CAMkiY3cSgf-tvft2tvDhVSBpYh17643Kszxp6RHSw-RqM5ndug@mail.gmail.com>

Hi Alfredo,

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

C?cile

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

> Hi C?cile,
>
> 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,
>
> C?cile
>
> On Thu, Sep 30, 2021 at 10:57 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Hi C?cile,
>>
>> 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?
>>
>> C?cile
>>
>> 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.
>>> The information in this e-mail is intended only for the person to whom
>>> it is addressed. If you believe this e-mail was sent to you in error and
>>> the e-mail contains patient information, please contact the Mass General
>>> Brigham Compliance HelpLine at
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>>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is addressed. If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Mass General
>> Brigham Compliance HelpLine at
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From sridar.narayanan at mcgill.ca  Mon Oct  4 14:30:05 2021
From: sridar.narayanan at mcgill.ca (Sridar Narayanan, Dr.)
Date: Mon, 4 Oct 2021 18:30:05 +0000
Subject: [Loris-dev] BIDS - AcquisitionType
In-Reply-To: <CAMkiY3cSgf-tvft2tvDhVSBpYh17643Kszxp6RHSw-RqM5ndug@mail.gmail.com>
References: <EC983D83-651E-4A10-B650-A25961C117D7@bwh.harvard.edu>
 <CAMkiY3dSF___LcDQj=fGua9wr9QgCUsmDKb6C6pBQkSQ-cbUEw@mail.gmail.com>
 <1431DEE0-4FC7-4B06-8EB5-BEDEF0A0E19B@bwh.harvard.edu>
 <CAMkiY3chweMnEt58ntpCXyBgF0MLx5rf9-MHwRSGR0s+coHBtA@mail.gmail.com>
 <32C3B4E3-E9A8-409C-8B6D-EF35E2794DB3@bwh.harvard.edu>
 <CAMkiY3cSgf-tvft2tvDhVSBpYh17643Kszxp6RHSw-RqM5ndug@mail.gmail.com>
Message-ID: <BC702306-F190-428C-ACE9-A78118AAE0B9@mcgill.ca>

Hi C?cile,

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>, Istv?n ?kos M?rocz <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.

C?cile

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 C?cile,

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,

C?cile

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 C?cile,

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?

C?cile

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.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1ig3dr6i1WdAs8_-Q_MeK7GXwa0dgT1TgKI1JS7MC0k4yUeF62G6kVevDIHZj5n8tYT0kmV7nj6Fy6sEMEe-xDkf6WhZtm0M-v0uUlyhiKd_DcQ1aSPrfn2jxfJIreAitqwR42XMZb84w7G5WECzE46VWrQ3SZQgrrNHlOq19WKP-mKl5SKE-kGJwNUp4d3l-NeVnWGOTeEoLAx7yXW4HO4FcWICnHaw7zpvritbMeXJqEIaabeQmg8ZEyf_niv71lNvwche53TaBWI6any_S-g/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1vNmj03p92XKeNCHdbzJ-j02hi9iHbmDxay9AX247pJJJvtYwtIZyiBHqc3DUdFuSQn-nLRXFZ7dK9HaISl9ToR42zIgDmGv42q0HWNyO2XbXVYuBO2blnxwrBHKNPEKpJXf6YZ5d86OueTBOIiPRNj-any8ibCsVdxK7Sju1vNDuN1iGp5AHOyUP_7nkK_UmAKzldlMZf9wxrrGxNW1bCF5SBeMzRLWc22DUtkJj__QzI9J1VVoJEscG6fZqitTlJgnLwTgWQRQLokaxkFBUxw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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From cecile.madjar at mcin.ca  Mon Oct  4 15:15:18 2021
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 4 Oct 2021 15:15:18 -0400
Subject: [Loris-dev] BIDS - AcquisitionType
In-Reply-To: <BC702306-F190-428C-ACE9-A78118AAE0B9@mcgill.ca>
References: <EC983D83-651E-4A10-B650-A25961C117D7@bwh.harvard.edu>
 <CAMkiY3dSF___LcDQj=fGua9wr9QgCUsmDKb6C6pBQkSQ-cbUEw@mail.gmail.com>
 <1431DEE0-4FC7-4B06-8EB5-BEDEF0A0E19B@bwh.harvard.edu>
 <CAMkiY3chweMnEt58ntpCXyBgF0MLx5rf9-MHwRSGR0s+coHBtA@mail.gmail.com>
 <32C3B4E3-E9A8-409C-8B6D-EF35E2794DB3@bwh.harvard.edu>
 <CAMkiY3cSgf-tvft2tvDhVSBpYh17643Kszxp6RHSw-RqM5ndug@mail.gmail.com>
 <BC702306-F190-428C-ACE9-A78118AAE0B9@mcgill.ca>
Message-ID: <CAMkiY3dk=115Ui+3U5+R+yucBFGVyyF74QdjMzfCaMLYp5q9XA@mail.gmail.com>

Hi Sridar,

Happy to help :-). Below are my answers to your 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?
>
> In the future, yes. I am actually developing a dcm2bids pipeline in my
spare time. I have made a lot of progress on this this summer but this is
not ready yet unfortunately. My deadline for this is this spring but I
really hope to have that ready sooner!! Maybe a little Christmas gift? ;-)

In the meantime however, outside of the standard imaging_upload_file.pl
pipeline, we have a script called imaging_non_minc_insertion.pl that allows
the insertion of NIfTI files along with a JSON sidecar file into LORIS. So
the pipeline could be tweaked to:
1) run dicom_archive/dicomTar.pl (instead of uploadNeuroDB/
imaging_upload_file.pl) to create the DICOM archives
2) create a tiny script to untar the DICOM archives and run dcm2niix (for
example to create the BIDS JSON sidecar along with the NIfTI file) on the
DICOMs.
3) run uploadNeuroDB/imaging_non_minc_insertion.pl on the NIfTI and JSON
files that were created with dcm2niix (or other converter equivalent).
Note: this imaging_non_minc_insertion.pl can be run on any file types other
than MINC as long as the proper options are provided to the script so that
LORIS knows to which candidate and visit the file should be attached and
with which scan type.


>
>    1.
>    2. If not, could we convert the BIDS/NIFTI files into MINC and upload
>    them, or will this conflict with the existing NIFTI files?
>
> I am not entirely sure to understand the question. You would want to do
dcm2nii and then nii2mnc?
Note: if there is already a file in the files table with the same
SeriesUID/EchoTime combination, then an error will be issued saying a scan
has already been inserted with the same SeriesUID/EchoTime combination. We
had to add the EchoTime field because we noticed that SeriesUID was not
unique for fieldmaps...


>
>    1.
>    2. Can the primary image upload be in MINC format? Up to now, we have
>    only uploaded MINC files for secondary data (e.g. masks).
>
> Yes, the script uploadNeuroDB/minc_insertion.pl can be called
independently to insert a MINC file directly. The script options are listed
when you run it with option -help

>
>    1.
>    2. 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.
>
> The STUDY_DCCID_VisitLabel_scan_type_counter.mnc is a LORIS convention for
the MINC files. The DICOMs are not organized under that naming structure
though because the processes run on the DICOM do not do candidate ID checks
and other validations on the DICOMs. This is done on the MINC/NIfTI level
only. However, in the tarchive_series and tarchive_files tables there is a
list of files with their SeriesUID and EchoTime so it can be easy to figure
out with database queries which DICOM files correspond to the inserted MINC
file.

Hope this helps! Let me know if you have any further questions.


> 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>, Istv?n ?kos M?rocz <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.
>
>
>
> C?cile
>
>
>
> On Mon, Oct 4, 2021 at 1:28 PM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Hi C?cile,
>
>
>
> 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,
>
>
>
> C?cile
>
>
>
> On Thu, Sep 30, 2021 at 10:57 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Hi C?cile,
>
>
>
> 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?
>
>
>
> C?cile
>
>
>
> 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.
>
> The information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and the
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> Brigham Compliance HelpLine at
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>
>
>
> The information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.org/complianceline
> <http://secure-web.cisco.com/1vNmj03p92XKeNCHdbzJ-j02hi9iHbmDxay9AX247pJJJvtYwtIZyiBHqc3DUdFuSQn-nLRXFZ7dK9HaISl9ToR42zIgDmGv42q0HWNyO2XbXVYuBO2blnxwrBHKNPEKpJXf6YZ5d86OueTBOIiPRNj-any8ibCsVdxK7Sju1vNDuN1iGp5AHOyUP_7nkK_UmAKzldlMZf9wxrrGxNW1bCF5SBeMzRLWc22DUtkJj__QzI9J1VVoJEscG6fZqitTlJgnLwTgWQRQLokaxkFBUxw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
> . If the e-mail was sent to you in error but does not contain patient
> information, please contact the sender and properly dispose of the e-mail.
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> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is addressed. If you believe this e-mail was sent to you in error and the
> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
> http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
>
>
>
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
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From sridar.narayanan at mcgill.ca  Mon Oct  4 15:23:54 2021
From: sridar.narayanan at mcgill.ca (Sridar Narayanan, Dr.)
Date: Mon, 4 Oct 2021 19:23:54 +0000
Subject: [Loris-dev] BIDS - AcquisitionType
In-Reply-To: <CAMkiY3dk=115Ui+3U5+R+yucBFGVyyF74QdjMzfCaMLYp5q9XA@mail.gmail.com>
References: <EC983D83-651E-4A10-B650-A25961C117D7@bwh.harvard.edu>
 <CAMkiY3dSF___LcDQj=fGua9wr9QgCUsmDKb6C6pBQkSQ-cbUEw@mail.gmail.com>
 <1431DEE0-4FC7-4B06-8EB5-BEDEF0A0E19B@bwh.harvard.edu>
 <CAMkiY3chweMnEt58ntpCXyBgF0MLx5rf9-MHwRSGR0s+coHBtA@mail.gmail.com>
 <32C3B4E3-E9A8-409C-8B6D-EF35E2794DB3@bwh.harvard.edu>
 <CAMkiY3cSgf-tvft2tvDhVSBpYh17643Kszxp6RHSw-RqM5ndug@mail.gmail.com>
 <BC702306-F190-428C-ACE9-A78118AAE0B9@mcgill.ca>
 <CAMkiY3dk=115Ui+3U5+R+yucBFGVyyF74QdjMzfCaMLYp5q9XA@mail.gmail.com>
Message-ID: <7668F919-3239-4F4C-9933-74DAF521DB29@mcgill.ca>

Hi Cecile,

Thanks, this is helpful. I think one important fact that you may not be aware of for this study (or may have forgotten) is that we only have BIDS data as our ?original? data. We don?t have access to the original DICOM files.

Would you be available to join a Zoom discussion we are having right now?

https://mcgill.zoom.us/j/85419914478?pwd=d0I1S2NKNUhBcmZKRURvZTRkN1Bvdz09

Thanks,

Sridar

From: Cecile Madjar <cecile.madjar at mcin.ca>
Date: Monday, October 4, 2021 at 3:15 PM
To: "Sridar Narayanan, Dr." <sridar.narayanan at mcgill.ca>
Cc: "Morales Pinzon, Alfredo" <AMORALESPINZON at bwh.harvard.edu>, "loris-dev at bic.mni.mcgill.ca" <loris-dev at bic.mni.mcgill.ca>, Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca>, "Douglas Arnold, Dr." <douglas.arnold at mcgill.ca>, "Guttmann Charles,M.D." <guttmann at bwh.harvard.edu>, Istv?n ?kos M?rocz <istvan.morocz at mcgill.ca>
Subject: Re: [Loris-dev] BIDS - AcquisitionType

Hi Sridar,

Happy to help :-). Below are my answers to your 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?
In the future, yes. I am actually developing a dcm2bids pipeline in my spare time. I have made a lot of progress on this this summer but this is not ready yet unfortunately. My deadline for this is this spring but I really hope to have that ready sooner!! Maybe a little Christmas gift? ;-)

In the meantime however, outside of the standard imaging_upload_file.pl<http://imaging_upload_file.pl> pipeline, we have a script called imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> that allows the insertion of NIfTI files along with a JSON sidecar file into LORIS. So the pipeline could be tweaked to:
1) run dicom_archive/dicomTar.pl (instead of uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl>) to create the DICOM archives
2) create a tiny script to untar the DICOM archives and run dcm2niix (for example to create the BIDS JSON sidecar along with the NIfTI file) on the DICOMs.
3) run uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> on the NIfTI and JSON files that were created with dcm2niix (or other converter equivalent). Note: this imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> can be run on any file types other than MINC as long as the proper options are provided to the script so that LORIS knows to which candidate and visit the file should be attached and with which scan type.


  1.
  2.  If not, could we convert the BIDS/NIFTI files into MINC and upload them, or will this conflict with the existing NIFTI files?
I am not entirely sure to understand the question. You would want to do dcm2nii and then nii2mnc?
Note: if there is already a file in the files table with the same SeriesUID/EchoTime combination, then an error will be issued saying a scan has already been inserted with the same SeriesUID/EchoTime combination. We had to add the EchoTime field because we noticed that SeriesUID was not unique for fieldmaps...


  1.
  2.  Can the primary image upload be in MINC format? Up to now, we have only uploaded MINC files for secondary data (e.g. masks).
Yes, the script uploadNeuroDB/minc_insertion.pl<http://minc_insertion.pl> can be called independently to insert a MINC file directly. The script options are listed when you run it with option -help

  1.
  2.  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.
The STUDY_DCCID_VisitLabel_scan_type_counter.mnc is a LORIS convention for the MINC files. The DICOMs are not organized under that naming structure though because the processes run on the DICOM do not do candidate ID checks and other validations on the DICOMs. This is done on the MINC/NIfTI level only. However, in the tarchive_series and tarchive_files tables there is a list of files with their SeriesUID and EchoTime so it can be easy to figure out with database queries which DICOM files correspond to the inserted MINC file.

Hope this helps! Let me know if you have any further questions.

Thanks,

Sridar


From: Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>>
Date: Monday, October 4, 2021 at 2:03 PM
To: "Morales Pinzon, Alfredo" <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>>
Cc: "loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>" <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>, Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca<mailto:rozie.arnaoutelis at mcgill.ca>>, "Sridar Narayanan, Dr." <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>>, "Douglas Arnold, Dr." <douglas.arnold at mcgill.ca<mailto:douglas.arnold at mcgill.ca>>, "Guttmann Charles,M.D." <guttmann at bwh.harvard.edu<mailto:guttmann at bwh.harvard.edu>>, Istv?n ?kos M?rocz <istvan.morocz at mcgill.ca<mailto: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.

C?cile

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 C?cile,

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,

C?cile

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 C?cile,

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?

C?cile

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.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1ig3dr6i1WdAs8_-Q_MeK7GXwa0dgT1TgKI1JS7MC0k4yUeF62G6kVevDIHZj5n8tYT0kmV7nj6Fy6sEMEe-xDkf6WhZtm0M-v0uUlyhiKd_DcQ1aSPrfn2jxfJIreAitqwR42XMZb84w7G5WECzE46VWrQ3SZQgrrNHlOq19WKP-mKl5SKE-kGJwNUp4d3l-NeVnWGOTeEoLAx7yXW4HO4FcWICnHaw7zpvritbMeXJqEIaabeQmg8ZEyf_niv71lNvwche53TaBWI6any_S-g/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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From sridar.narayanan at mcgill.ca  Tue Oct 12 11:49:03 2021
From: sridar.narayanan at mcgill.ca (Sridar Narayanan, Dr.)
Date: Tue, 12 Oct 2021 15:49:03 +0000
Subject: [Loris-dev] BIDS - AcquisitionType & MINC conversion
Message-ID: <DBD132E4-4075-42F5-82EA-62C4EA86A33A@mcgill.ca>

Hi Cecile,

I hope you had a good weekend. We were wondering whether you had discussed with Samir whether you would be able to devote some time to implementing a BIDS/Nifti to MINC converter within LORIS?

Thanks,

Sridar

From: "Sridar Narayanan, Dr." <sridar.narayanan at mcgill.ca>
Date: Monday, October 4, 2021 at 3:23 PM
To: Cecile Madjar <cecile.madjar at mcin.ca>
Cc: "Morales Pinzon, Alfredo" <AMORALESPINZON at bwh.harvard.edu>, "loris-dev at bic.mni.mcgill.ca" <loris-dev at bic.mni.mcgill.ca>, Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca>, "Douglas Arnold, Dr." <douglas.arnold at mcgill.ca>, "Guttmann Charles,M.D." <guttmann at bwh.harvard.edu>, Istv?n ?kos M?rocz <istvan.morocz at mcgill.ca>
Subject: Re: [Loris-dev] BIDS - AcquisitionType

Hi Cecile,

Thanks, this is helpful. I think one important fact that you may not be aware of for this study (or may have forgotten) is that we only have BIDS data as our ?original? data. We don?t have access to the original DICOM files.

Would you be available to join a Zoom discussion we are having right now?

https://mcgill.zoom.us/j/85419914478?pwd=d0I1S2NKNUhBcmZKRURvZTRkN1Bvdz09

Thanks,

Sridar

From: Cecile Madjar <cecile.madjar at mcin.ca>
Date: Monday, October 4, 2021 at 3:15 PM
To: "Sridar Narayanan, Dr." <sridar.narayanan at mcgill.ca>
Cc: "Morales Pinzon, Alfredo" <AMORALESPINZON at bwh.harvard.edu>, "loris-dev at bic.mni.mcgill.ca" <loris-dev at bic.mni.mcgill.ca>, Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca>, "Douglas Arnold, Dr." <douglas.arnold at mcgill.ca>, "Guttmann Charles,M.D." <guttmann at bwh.harvard.edu>, Istv?n ?kos M?rocz <istvan.morocz at mcgill.ca>
Subject: Re: [Loris-dev] BIDS - AcquisitionType

Hi Sridar,

Happy to help :-). Below are my answers to your 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?
In the future, yes. I am actually developing a dcm2bids pipeline in my spare time. I have made a lot of progress on this this summer but this is not ready yet unfortunately. My deadline for this is this spring but I really hope to have that ready sooner!! Maybe a little Christmas gift? ;-)

In the meantime however, outside of the standard imaging_upload_file.pl<http://imaging_upload_file.pl> pipeline, we have a script called imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> that allows the insertion of NIfTI files along with a JSON sidecar file into LORIS. So the pipeline could be tweaked to:
1) run dicom_archive/dicomTar.pl (instead of uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl>) to create the DICOM archives
2) create a tiny script to untar the DICOM archives and run dcm2niix (for example to create the BIDS JSON sidecar along with the NIfTI file) on the DICOMs.
3) run uploadNeuroDB/imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> on the NIfTI and JSON files that were created with dcm2niix (or other converter equivalent). Note: this imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl> can be run on any file types other than MINC as long as the proper options are provided to the script so that LORIS knows to which candidate and visit the file should be attached and with which scan type.


  1.
  2.  If not, could we convert the BIDS/NIFTI files into MINC and upload them, or will this conflict with the existing NIFTI files?
I am not entirely sure to understand the question. You would want to do dcm2nii and then nii2mnc?
Note: if there is already a file in the files table with the same SeriesUID/EchoTime combination, then an error will be issued saying a scan has already been inserted with the same SeriesUID/EchoTime combination. We had to add the EchoTime field because we noticed that SeriesUID was not unique for fieldmaps...


  1.
  2.  Can the primary image upload be in MINC format? Up to now, we have only uploaded MINC files for secondary data (e.g. masks).
Yes, the script uploadNeuroDB/minc_insertion.pl<http://minc_insertion.pl> can be called independently to insert a MINC file directly. The script options are listed when you run it with option -help

  1.
  2.  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.
The STUDY_DCCID_VisitLabel_scan_type_counter.mnc is a LORIS convention for the MINC files. The DICOMs are not organized under that naming structure though because the processes run on the DICOM do not do candidate ID checks and other validations on the DICOMs. This is done on the MINC/NIfTI level only. However, in the tarchive_series and tarchive_files tables there is a list of files with their SeriesUID and EchoTime so it can be easy to figure out with database queries which DICOM files correspond to the inserted MINC file.

Hope this helps! Let me know if you have any further questions.

Thanks,

Sridar


From: Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>>
Date: Monday, October 4, 2021 at 2:03 PM
To: "Morales Pinzon, Alfredo" <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>>
Cc: "loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>" <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>, Rozie Arnaoutelis <rozie.arnaoutelis at mcgill.ca<mailto:rozie.arnaoutelis at mcgill.ca>>, "Sridar Narayanan, Dr." <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>>, "Douglas Arnold, Dr." <douglas.arnold at mcgill.ca<mailto:douglas.arnold at mcgill.ca>>, "Guttmann Charles,M.D." <guttmann at bwh.harvard.edu<mailto:guttmann at bwh.harvard.edu>>, Istv?n ?kos M?rocz <istvan.morocz at mcgill.ca<mailto: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.

C?cile

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 C?cile,

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,

C?cile

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 C?cile,

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?

C?cile

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.
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1ig3dr6i1WdAs8_-Q_MeK7GXwa0dgT1TgKI1JS7MC0k4yUeF62G6kVevDIHZj5n8tYT0kmV7nj6Fy6sEMEe-xDkf6WhZtm0M-v0uUlyhiKd_DcQ1aSPrfn2jxfJIreAitqwR42XMZb84w7G5WECzE46VWrQ3SZQgrrNHlOq19WKP-mKl5SKE-kGJwNUp4d3l-NeVnWGOTeEoLAx7yXW4HO4FcWICnHaw7zpvritbMeXJqEIaabeQmg8ZEyf_niv71lNvwche53TaBWI6any_S-g/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev<https://secure-web.cisco.com/1d3CFTBToT4j_It30C0sMIZMcTjPqg9RYBFR977oo5ohdasD5Q6U_0ZthyISkUY7Scl8QHwLUGl1JPlpSq6nGt24dMn4qVx8wLxa2UEgaCQgBVAFsdSgusVbLZfj66xn8uFJW_6Qn157m_S9eVZtPrTxUxdhnqC-Yle4xue7mwU5VhzucMFWdxp7uxzLYfwjG35JojFFEy8Aa2x9j2hSO3E-NPuUnrYeqQtR4GFLMRpTbp_8xv4S_0T1hH6fYlqR6JyiOCvcB7AV9LbjIr5GAkQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev>

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline<http://secure-web.cisco.com/1vNmj03p92XKeNCHdbzJ-j02hi9iHbmDxay9AX247pJJJvtYwtIZyiBHqc3DUdFuSQn-nLRXFZ7dK9HaISl9ToR42zIgDmGv42q0HWNyO2XbXVYuBO2blnxwrBHKNPEKpJXf6YZ5d86OueTBOIiPRNj-any8ibCsVdxK7Sju1vNDuN1iGp5AHOyUP_7nkK_UmAKzldlMZf9wxrrGxNW1bCF5SBeMzRLWc22DUtkJj__QzI9J1VVoJEscG6fZqitTlJgnLwTgWQRQLokaxkFBUxw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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From mndmazaheri at gmail.com  Wed Oct 20 17:00:32 2021
From: mndmazaheri at gmail.com (mandana mazaheri)
Date: Wed, 20 Oct 2021 14:00:32 -0700
Subject: [Loris-dev] what is loris url?
Message-ID: <CALw_=Q0+yQfjrcgLVvxphyc1bkPFF5EQW5OYyDa36hEFi1dqsA@mail.gmail.com>

Dear LORIS team,

I am installing LORIS DEV and need to what exactly is the  <loris-url> and
<front-end-loris-url> to access /installdb.php?

Best
Mandana
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From rida.abou-haidar at mcin.ca  Wed Oct 20 20:01:14 2021
From: rida.abou-haidar at mcin.ca (Rida Abou-Haidar)
Date: Wed, 20 Oct 2021 20:01:14 -0400
Subject: [Loris-dev] what is loris url?
In-Reply-To: <CALw_=Q0+yQfjrcgLVvxphyc1bkPFF5EQW5OYyDa36hEFi1dqsA@mail.gmail.com>
References: <CALw_=Q0+yQfjrcgLVvxphyc1bkPFF5EQW5OYyDa36hEFi1dqsA@mail.gmail.com>
Message-ID: <CABbkjAg7TXFHjitWF4S2uXnkNZ2jtPPj5N8azKRK8TZFQHAVsg@mail.gmail.com>

Hi Mandana,

 Have you been added to the slack channel ? If ao send me a message there
and we will go through this.

Best,
Rida Abou-Haidar
Software Developer
Montreal Neurological Institute
McGill University
rida.abou-haidar at mcin.ca

On Wed., Oct. 20, 2021, 5:01 p.m. mandana mazaheri <mndmazaheri at gmail.com>
wrote:

> Dear LORIS team,
>
> I am installing LORIS DEV and need to what exactly is the  <loris-url> and
> <front-end-loris-url> to access /installdb.php?
>
> Best
> Mandana
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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From dave.macfarlane at mcin.ca  Thu Oct 21 09:02:50 2021
From: dave.macfarlane at mcin.ca (Dave MacFarlane)
Date: Thu, 21 Oct 2021 09:02:50 -0400
Subject: [Loris-dev] what is loris url?
In-Reply-To: <CALw_=Q0+yQfjrcgLVvxphyc1bkPFF5EQW5OYyDa36hEFi1dqsA@mail.gmail.com>
References: <CALw_=Q0+yQfjrcgLVvxphyc1bkPFF5EQW5OYyDa36hEFi1dqsA@mail.gmail.com>
Message-ID: <CAN9cDwHrNFRxzjMuCcnRUvM1qFH=6yKUv2SbU0mypTY6HNTbFw@mail.gmail.com>

Hi Mandana,

Where are you seeing those terms? "<loris-url>" in the LORIS README refers
to the URL that you use to access your LORIS web server but I don't see
"front-end-loris-url" used.

On Wed, Oct 20, 2021 at 5:01 PM mandana mazaheri <mndmazaheri at gmail.com>
wrote:

> Dear LORIS team,
>
> I am installing LORIS DEV and need to what exactly is the  <loris-url> and
> <front-end-loris-url> to access /installdb.php?
>
> Best
> Mandana
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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From Yiwen.Tian at nki.rfmh.org  Wed Oct 27 14:11:59 2021
From: Yiwen.Tian at nki.rfmh.org (Tian, Yiwen (NKI))
Date: Wed, 27 Oct 2021 18:11:59 +0000
Subject: [Loris-dev] Installing Email Server
Message-ID: <PH0PR09MB7932DCBA9FC11531C4461F71AD859@PH0PR09MB7932.namprd09.prod.outlook.com>

Hi LorisDev Team,

I wonder if you have a guide for installing a email server that works with loris frontend? I wasn't able to find anything online. Anything helps! Thank you!

Best,
Yiwen

________________________________

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From melanie.legault2 at mcgill.ca  Wed Oct 27 14:27:06 2021
From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs)
Date: Wed, 27 Oct 2021 18:27:06 +0000
Subject: [Loris-dev] Installing Email Server
In-Reply-To: <PH0PR09MB7932DCBA9FC11531C4461F71AD859@PH0PR09MB7932.namprd09.prod.outlook.com>
References: <PH0PR09MB7932DCBA9FC11531C4461F71AD859@PH0PR09MB7932.namprd09.prod.outlook.com>
Message-ID: <YQBPR0101MB455592BF3687D1638D0D8BCECF859@YQBPR0101MB4555.CANPRD01.PROD.OUTLOOK.COM>

Hello Yimen,

I suggest you to contact your local IT team. They surely already have a mail server that you can use.

If you do wish to install your own mail server, there is the venerable SendMail or the excellent Exim mail server that you can use.
You will find lots of information on how to set them up on the web.
Having your own mail server will add lot of burden on your shoulder as not only another piece of software to manage but also take care of the spam, security, regular update, ...

Kind regards,
M?lanie


________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Tian, Yiwen (NKI) <Yiwen.Tian at nki.rfmh.org>
Sent: October 27, 2021 14:11
To: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
Subject: [Loris-dev] Installing Email Server

Hi LorisDev Team,

I wonder if you have a guide for installing a email server that works with loris frontend? I wasn't able to find anything online. Anything helps! Thank you!

Best,
Yiwen

________________________________

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From mndmazaheri at gmail.com  Fri Oct 29 19:12:19 2021
From: mndmazaheri at gmail.com (mandana mazaheri)
Date: Fri, 29 Oct 2021 16:12:19 -0700
Subject: [Loris-dev] failed uploading through imaging Uploader module
Message-ID: <CALw_=Q0DHfqZWLUkDJ6tAjKta7EWepraGigifUOytk=Wk5awEA@mail.gmail.com>

Hi LorisDev Team,

I am trying to upload a compressed file (zip) through Imaging Uploader in
the LORIS frontend, but I get the following error message, could you assist
me with how I should proceed?
[image: image.png]
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