[Loris-dev] LORIS - Upload nifti and minc

Tue Jan 26 16:49:23 EST 2021

Hi Cecile,

Yes, that is very helpful.

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).

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?

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?

Thanks!

Sridar

On Jan 26, 2021, at 4:33 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:

Hi,

Thank you for the clarification. I think I understand better the confusion.

You can insert MINC files without having to insert DICOM files by running the minc_insertion.pl<http://minc_insertion.pl/> script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to.

minc_insertion.pl<http://minc_insertion.pl/> -profile <name of your profile file, typically prod> -mincPath <path to your MINC file> -force -create_minc_pics

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 imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> (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 imaging_non_minc_insertion.pl<http://imaging_non_minc_insertion.pl/> on the loaded NIfTI files.

Does that clarify the steps?

Thanks!

Cécile

On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>> wrote:
Hi Cecile,

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 instead of importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can avoid importing DICOM 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).

Thanks,

Sridar

On Jan 25, 2021, at 5:01 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:

Hi Alfredo,

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?

Sorry, maybe I am missing something.

Cécile

On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cecile,

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.

Do you have scripts for this?

Best,
Alfredo.

On Jan 19, 2021, at 1:59 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:

        External Email - Use Caution

Hi Alfredo,

Very sorry for the late reply. In short, yes, it is possible to do both.

It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl<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> in the uploadNeuroDB folder. If you run perl minc_insertion.pl<http://secure-web.cisco.com/13jgtqDYN7Gf_vgFThFhtlVEFqhsVru-JRquRrfzp92y9hcK9koGa9r9E_RCEHuDzqw9ZQq4eWBdGe5cbbKU8_yrxXgz98kTVTBySSdwUF3dgAiL6ls9glxHxeHwLfR-M9U6DLj3ePJR758eO7Ukl-KBwGCnH1TTfOmLDAPWxs4ABKnOnHa0AHFN4qsRIDO6BMvq5wK_o-G0mjUXNUyb7jkUjg-xsaAHbLYjZ1X15d3pWFi0jmNTPfm57PC77a41n7xp5Ae2Ji6UtzrGAczTtBg/http%3A%2F%2Fminc_insertion.pl> -h; you will see the explanation on how to run the script.

Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl<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> in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl<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> should give you all the information you need in order to run the script.

Hope this helps,

Cécile

On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LorisDev team,

Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format?

Best regards,
Alfredo.
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