[Loris-dev] LORIS - Upload nifti and minc

[Cecile Madjar]

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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> is addressed. If you believe this e-mail was sent to you in error and the
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