[Loris-dev] LORIS - Upload nifti and minc

Tue Jan 26 16:33:51 EST 2021

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 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 -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
(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
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> 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> 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> 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> 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> 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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>>
>> 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.
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