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<p class="MsoNormal">Hi Cécile,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for answering Alfredo’s questions. I have a couple of additional questions.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<ol style="margin-top:0cm" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1">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?<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1">If not, could we convert the BIDS/NIFTI files into MINC and upload them, or will this conflict with the existing NIFTI files?<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1">Can the primary image upload be in MINC format? Up to now, we have only uploaded MINC files for secondary data (e.g. masks).<o:p></o:p></li><li class="MsoListParagraph" style="margin-left:0cm;mso-list:l0 level1 lfo1">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 <b>Pisti</b>, 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.<o:p></o:p></li></ol>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sridar<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Cecile Madjar <cecile.madjar@mcin.ca><br>
<b>Date: </b>Monday, October 4, 2021 at 2:03 PM<br>
<b>To: </b>"Morales Pinzon, Alfredo" <AMORALESPINZON@bwh.harvard.edu><br>
<b>Cc: </b>"loris-dev@bic.mni.mcgill.ca" <loris-dev@bic.mni.mcgill.ca>, Rozie Arnaoutelis <rozie.arnaoutelis@mcgill.ca>, "Sridar Narayanan, Dr." <sridar.narayanan@mcgill.ca>, "Douglas Arnold, Dr." <douglas.arnold@mcgill.ca>, "Guttmann Charles,M.D." <guttmann@bwh.harvard.edu>,
István Ákos Mórocz <istvan.morocz@mcgill.ca><br>
<b>Subject: </b>Re: [Loris-dev] BIDS - AcquisitionType<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Hi Alfredo,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Indeed, you could change the AcquisitionProtoolID in the files table so that it points to the t1g scan type.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Cécile<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Mon, Oct 4, 2021 at 1:28 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<o:p></o:p></p>
</div>
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<p class="MsoNormal">Hi Cécile, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thank you for the explanation, I will use this solution for a future dataset.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">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?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Alfredo.<o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Oct 1, 2021, at 4:51 PM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Hi Alfredo, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I found the line of code that set the scan type to the BIDS suffix in LORIS-MRI: <a href="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" target="_blank">https://github.com/aces/Loris-MRI/blob/c69c89d0c64838e4a174b4a267a1406ce724878a/python/lib/mri.py#L279</a> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">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. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">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.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Does that make sense? <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Hope this helps,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Cécile<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Thu, Sep 30, 2021 at 10:57 AM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<o:p></o:p></p>
</div>
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<p class="MsoNormal">Hi Cécile, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">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.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Alfredo.<o:p></o:p></p>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Aug 17, 2021, at 9:04 AM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank">cecile.madjar@mcin.ca</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Hi Alfredo, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">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.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">If you really want to add the acq prefix to the scan type, you could always modify this
<a href="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" target="_blank">
line of code</a> so that it also takes the acq prefix when looking for a scan type?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Cécile <o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Mon, Aug 16, 2021 at 3:51 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<o:p></o:p></p>
</div>
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<div>
<p class="MsoNormal">Dear LorisDev team, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I have a question regarding the AcquisitionType assigned to images imported using the BIDS functionality: how do you assign the AcquisitionType?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">For some cases it looks good, but some it doesn’t match the “acq” label in BIDS:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Example of correct acquisition type:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">===<o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"> {<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> "OutputType": "native",<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> "Filename": "sub-BGK104001_ses-month36_run-2_<span style="color:black;background:red">T1w</span>.nii.gz",<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> "AcquisitionType": "<span style="color:black;background:red">T1w</span>"<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> }<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal">===<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Example of wrong acquisition type, in this case it should be
<span style="color:black;background:red">MT0</span>.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">===<o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"> {<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> "OutputType": "native",<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> "Filename": "sub-BGK104001_ses-month36_acq-<span style="color:black;background:red">MT0</span>_run-1_T2w.nii.gz",<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> "AcquisitionType": "t2w"<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> },<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal">===<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Would it be possible to modify the way the acquisition types are being assigned so that it takes the “acq” label from BIDS?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thank you for your help.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best regards,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Alfredo.<o:p></o:p></p>
</div>
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<p class="MsoNormal">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 <a href="http://secure-web.cisco.com/1vNmj03p92XKeNCHdbzJ-j02hi9iHbmDxay9AX247pJJJvtYwtIZyiBHqc3DUdFuSQn-nLRXFZ7dK9HaISl9ToR42zIgDmGv42q0HWNyO2XbXVYuBO2blnxwrBHKNPEKpJXf6YZ5d86OueTBOIiPRNj-any8ibCsVdxK7Sju1vNDuN1iGp5AHOyUP_7nkK_UmAKzldlMZf9wxrrGxNW1bCF5SBeMzRLWc22DUtkJj__QzI9J1VVoJEscG6fZqitTlJgnLwTgWQRQLokaxkFBUxw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline" target="_blank">
http://www.massgeneralbrigham.org/complianceline</a> . 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.<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.
<o:p></o:p></p>
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</blockquote>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">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 <a href="http://www.massgeneralbrigham.org/complianceline" target="_blank">
http://www.massgeneralbrigham.org/complianceline</a> . 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.<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.
<o:p></o:p></p>
</div>
</blockquote>
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