[Loris-dev] IMAGE UPLOAD FAILURE

Thu Jun 29 12:18:38 EDT 2023

Hi Maria!

Automatic processing of the uploaded scans is not enabled by default. To
enable it, log into LORIS and access the Admin -> Configuration module.
Then click on the 'Study' label on the left side of the page and set
'ImagingUploader Auto Launch' to 'Yes'. I suggest you process a couple of
scans manually before using this feature though, just to make sure that
your MRI pipeline is set up correctly and works as expected. Script
imaging_upload_file.pl is indeed the script to run to process an
uploaded scan archive. Refer to
https://github.com/aces/Loris-MRI/blob/main/docs/05-PipelineLaunchOptions.md#511-option-1
for
instructions on how to use this script. Please make sure that your
LORIS-MRI is installed and configured correctly before proceeding. You'll
also find a lot of useful information on scan processing in LORIS here:
https://github.com/aces/Loris-MRI.

Let me know if you have any questions or if you still need to have a Zoom
chat.

Best regards,
Nicolas

On Thu, Jun 29, 2023 at 6:56 AM Olano.María <molano at ext.cnio.es> wrote:

> Hi Nicolas!
>
>
>
> We simply uploaded our image through the frontend Imaging Uploader as it
> automatically starts the process of creating the MySQL line and
> information, and then used the imaging_non_minc_insertion.pl . Was
> unaware of the imaging_file_upload.pl script, and maybe that is the key
> to making it work.
>
>
>
> Would you be available today at 10 AM your time? (4 PM mine)
>
>
>
> Best,
>
>
>
> María
>
>
>
> *From:* Nicolas Brossard <nicolasbrossard.mni at gmail.com>
> *Sent:* 28 June 2023 17:49
> *To:* Olano.María <molano at ext.cnio.es>
> *Cc:* loris-dev at bic.mni.mcgill.ca
> *Subject:* Re: [Loris-dev] IMAGE UPLOAD FAILURE
>
>
>
> *CAUTION: This email originated from outside of the organization. Do not
> click links or open attachments unless you recognize the sender and know
> the content is safe*
>
>
>
> Hi Maria,
>
>
>
> In the commands you mentioned in your first email, you refer to an upload
> with ID 1. Did you process this upload with script imaging_file_upload.pl?
> This should be the first thing to do. Script imaging_non_minc_insertion.pl
> should only be used for "non-standard" insertions that could not be done
> using this process. Also, when you run script imaging_file_upload.pl, it
> will create an image for every modality that it successfully processed so
> you should not have to manually insert the images yourself.
>
>
>
> I think I need to see the big picture in order to diagnose this issue.
> Would you be available for a Zoom call? I assume you are in Spain so
> there's a ~6 hour time difference (your 5PM is my 11AM). I gots lots of
> time for this so send me an invite and we'll take it from there.
>
>
>
> Best,
>
> Nicolas
>
>
>
> On Wed, Jun 28, 2023 at 2:46 AM Olano.María <molano at ext.cnio.es> wrote:
>
> Hi Nicolas!
>
>
>
> Thank you very much for your help! No, there is only one image in the zip
> file we are trying to insert.
>
>
>
> Best regards,
>
>
>
> María
> ------------------------------
>
> *From:* Nicolas Brossard <nicolasbrossard.mni at gmail.com>
> *Sent:* Tuesday, June 27, 2023 7:38 PM
> *To:* Olano.María <molano at ext.cnio.es>
> *Cc:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
> *Subject:* Re: [Loris-dev] IMAGE UPLOAD FAILURE
>
>
>
> *CAUTION: This email originated from outside of the organization. Do not
> click links or open attachments unless you recognize the sender and know
> the content is safe*
>
>
>
> Hi Maria,
>
>
>
> I'll be helping you debug this. The script imaging_non_minc_insertion.pl
> is used to insert *one* non-minc file into the database. Are there files
> other than the image file inside your zip archive or is it the only file?
>
>
>
>
>
> Best,
>
> Nicolas
>
>
>
> On Mon, Jun 26, 2023 at 9:08 AM Olano.María <molano at ext.cnio.es> wrote:
>
> Hello!
>
>
>
> We have followed the imaging upload process throught the *imaging_non_minc_insertion.pl
> <http://imaging_non_minc_insertion.pl> *script and unfortunately we are
> unable to see the image associated to the patient. This is what we typed
> into the cmd and the response.
>
>
>
> *uploadNeuroDB/imaging_non_minc_insertion.pl
> <http://imaging_non_minc_insertion.pl> -profile prod -upload_id 1
> -file_path /data/casadp/data/157011001_223572_PathologicalPancreas.zip
> -output_type native -scan_type he -date_acquired 2012-04-20 -scanner_id 1
> -coordin_space native -reckless -verbose -patient_name
> 157011001_223572_PathologicalPancreas*
>
>
>
> *log dir is /data/casadp/data/logs and log file is
> /data/casadp/data/logs/FileLoad-9-55-_KU5t4.log.*
>
> *PSCID is: 157011001*
>
> *CandID id: 223572*
>
> *visit_label is: PathologicalPancreas*
>
> *PSCID is: 157011001*
>
> *CandID id: 223572*
>
> *visit_label is: PathologicalPancreas*
>
> *    -> ScannerID was set to 1*
>
>
>
> *    -> SessionID was set to 2*
>
>
>
> *    -> Acquisition date was set to 2012-04-20*
>
>
>
> *    -> Output type was set to native*
>
> *Acquisition date: 2012-04-20*
>
>
>
> When seeing the log dir this is what greets us
>
> *==> computing md5 hash for MINC body.*
>
>
>
> *--> md5: ac8645a1c1a1619d712e0703cdde22cd*
>
>
>
> *File /data/casadp/data/157011001_223572_PathologicalPancreas.zip*
>
> *moved to:*
>
>
> */data/casadp/data/assembly/223572/PathologicalPancreas/mri/native/casadp_223572_PathologicalPancreas_he_001.zip*
>
>
>
> And the image is indeed in that path. However, when we return to our
> frontend, it says there is no imaging data available. Is there a step we
> haven’t followed?
>
>
>
> If you have any suggestions as to what to do, we’d be more than happy to
> hear it.
>
>
>
> Thank you in advance!
>
>
>
> María
>
>
>
>
>
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> el objeto del presente mensaje. Estos datos personales no serán comunicados
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> la protección de los datos personales de las personas físicas, la
> información personal que nos pueda facilitar a través de este correo
> electrónico quedará registrada por la Fundación CNIO con la finalidad de
> tramitar el objeto del presente correo electrónico. El tratamiento de sus
> datos personales se encuentra legitimado por ser necesario para gestionar
> el objeto del presente mensaje. Estos datos personales no serán comunicados
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> exigido por una ley. Ud. podrá ejercer los derechos de acceso,
> rectificación, supresión, limitación de tratamiento, portabilidad y
> oposición en la siguiente dirección: c/Melchor Fernandez Almagro 3, 28029
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