[Loris-dev] LORIS - Upload nifti and minc

Tue Jan 26 17:21:36 EST 2021

Hi,

Indeed, after importing the MINC file, a NIfTI file can be created and
associated with it by running the mass_nii.pl script on a range of FileIDs.
Be sure to have the configuration option "Create NIfTI files" set to yes in
the imaging pipeline part of the config module. Although, this is probably
the case if you were having MINC + NIfTI with DICOM uploads.

In LORIS-MRI, there is also a python pipeline (bids_import.py in the python
directory) that allows the import of BIDS datasets (EEG and MRI currently
supported). Unfortunately, we do not have a BIDS to MINC converter though.

However, we have an example tool to convert MINC files into a BIDS dataset
but it has to be customized for each project depending on the acquisition
particulars.

Hope this helps,

Cécile

On Tue, Jan 26, 2021 at 4:49 PM Sridar Narayanan, Dr. <
sridar.narayanan at mcgill.ca> wrote:

> 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> 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 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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>>
>>
>
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