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Hi Cecile,
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<div class="">Yes, that is very helpful.</div>
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<div class="">We would not import a NIfTI file alone, however. The options would be: MINC + NIfTI; BIDS alone; BIDS + MINC (if the BIDS import does not create a MINC file automatically).</div>
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<div class="">My understanding is that when DICOM files are imported for a new visit, both a MINC file and a NIfTI file are created automatically. If, instead of importing DICOM, a MINC file is imported, will a corresponding NIfTI file also be created internally?
If not, can we just attached the NIfTI file to the record created when the MINC file is uploaded?</div>
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<div class="">What happens when a BIDS file is imported - will a MINC file also be created, or would BIDS be the only image representation? Are BIDS to MINC converters available?</div>
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<div class="">Thanks!</div>
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<div class="">Sridar</div>
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<div class="">On Jan 26, 2021, at 4:33 PM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
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<div dir="ltr" class="">Hi,
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<div class="">Thank you for the clarification. I think I understand better the confusion.</div>
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<div class="">You can insert MINC files without having to insert DICOM files by running the
<a href="http://minc_insertion.pl/" class="">minc_insertion.pl</a> script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to.</div>
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<div class=""><a href="http://minc_insertion.pl/" class="">minc_insertion.pl</a> -profile <name of your profile file, typically prod> -mincPath <path to your MINC file> -force -create_minc_pics</div>
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<div class="">For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script <a href="http://imaging_non_minc_insertion.pl/" class="">imaging_non_minc_insertion.pl</a>
(output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files.
It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run
<a href="http://imaging_non_minc_insertion.pl/" class="">imaging_non_minc_insertion.pl</a> on the loaded NIfTI files.</div>
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<div class="">Does that clarify the steps? </div>
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<div class="">Thanks!</div>
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<div class="">Cécile</div>
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<div dir="ltr" class="gmail_attr">On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. <<a href="mailto:sridar.narayanan@mcgill.ca" class="">sridar.narayanan@mcgill.ca</a>> wrote:<br class="">
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<div style="overflow-wrap: break-word;" class="">Hi Cecile,
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<div class="">Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible
to import MRI data into Loris as MINC & NifTI files <u class="">instead of</u> importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can
<u class="">avoid importing DICOM</u> for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done
(e.g. for label files associated with the images).</div>
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<div class="">Thanks,</div>
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<div class="">Sridar</div>
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<div class="">On Jan 25, 2021, at 5:01 PM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
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<div dir="ltr" class="">Hi Alfredo,
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<div class="">I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them?</div>
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<div class="">Sorry, maybe I am missing something.</div>
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<div class="">Cécile</div>
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<div dir="ltr" class="gmail_attr">On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br class="">
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<div class="">Hi Cecile,
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<div class="">Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the “raw” images in minc and nifti images instead of DICOM. We are having a lot of issues
importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar.</div>
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<div class="">Do you have scripts for this?</div>
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<div class="">Best,</div>
<div class="">Alfredo.<br class="">
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<div class="">On Jan 19, 2021, at 1:59 PM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
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<p class=""><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)" class=""> External Email - Use Caution </span></p>
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<div dir="ltr" class="">Hi Alfredo,
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<div class="">Very sorry for the late reply. In short, yes, it is possible to do both.</div>
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<div class="">It is possible to insert MINC files in LORIS by using the LORIS-MRI script called
<a href="https://secure-web.cisco.com/1h8RHj_R4mnovi1vzHjXIG7OriE5SmwPXivIa6upEGgUmO0oyYw5rNJDqM2MdvPGvTNW0VgU36iIDos755qEXc2ZLdcGpGZQRfXLN_QGCSHqe5_pR8SPcRCLVkIkUT9JFyTm2tgFJomSHtiCakjIicPSDvv5QaC2BEX0O8gPHeY_UrixP8DhG29aU9BwThbmfsNCgJS9rWE8hkKiSJu3dXUWYZuz3SELo6A5cEG3a0urWWaEYKsL-uNUUQlpn-dLXHjrf4KywfR-f_8XtyxHIrA/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2FuploadNeuroDB%2Fminc_insertion.pl" target="_blank" class="">
minc_insertion.pl</a> in the uploadNeuroDB folder. If you run perl <a href="http://secure-web.cisco.com/13jgtqDYN7Gf_vgFThFhtlVEFqhsVru-JRquRrfzp92y9hcK9koGa9r9E_RCEHuDzqw9ZQq4eWBdGe5cbbKU8_yrxXgz98kTVTBySSdwUF3dgAiL6ls9glxHxeHwLfR-M9U6DLj3ePJR758eO7Ukl-KBwGCnH1TTfOmLDAPWxs4ABKnOnHa0AHFN4qsRIDO6BMvq5wK_o-G0mjUXNUyb7jkUjg-xsaAHbLYjZ1X15d3pWFi0jmNTPfm57PC77a41n7xp5Ae2Ji6UtzrGAczTtBg/http%3A%2F%2Fminc_insertion.pl" target="_blank" class="">
minc_insertion.pl</a> -h; you will see the explanation on how to run the script.</div>
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<div class="">Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called
<a href="https://secure-web.cisco.com/11rMDfTbsxeYelAro9qFHffjunl6PQySl-cFRkp1QAl_sinKZ_2ULH-80TnkR2omX6h5c78cX8Vvl4xgml5nGxkii9oOTjLtfmZO4NsBu-w2Dxh2E5l5p4rjx9RKrSRQak24h8B8rvl1sVWzkBe5qftWBHEd1FCLV4ptJPdCzV7xqJf3fMCIGfs77Mk6WCmGBhuL0FPSHDnWmRRvXzXAT5wH5eAUsHI3_2F8yAh25Hpvd-t9vttu-mAGU_XbLNQXQf2DNBFxGjThITPI2ptn38Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2FuploadNeuroDB%2Fimaging_non_minc_insertion.pl" target="_blank" class="">
imaging_non_minc_insertion.pl</a> in the same uploadNeuroDB folder. Running perl <a href="http://secure-web.cisco.com/1JUwbjz4V-PmM1LkrSIDPw4ydwAZ7otVSJadvo40dcrQMsYYfCLZsWRbpIcZwOZ3-TV3DyLARQX4Fp7-IHGmufed_LFzA0ah5UuJSegiZBGWQE9RiKXU6LxPe9xHqMfhyirSZF4zFetUaHoOtn5Pa9lFbV5o2FFI95zKG4NrmEX-HgUA_dMYmHrIFagQBzH_uujh-hUSiWM7Hvbf_d_KanWYNOrmkjAoe07MI18KuH0XsY5Gmhap81i-fVggYZHLthuCTL9_Dpky-ZNaeiyOlZw/http%3A%2F%2Fimaging_non_minc_insertion.pl" target="_blank" class="">
imaging_non_minc_insertion.pl</a> should give you all the information you need in order to run the script.</div>
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<div class="">Hope this helps,</div>
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<div class="">Cécile</div>
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<div dir="ltr" class="gmail_attr">On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br class="">
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Dear LorisDev team,<br class="">
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Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format?<br class="">
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Best regards,<br class="">
Alfredo.<br class="">
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