From xavier.lecoursboucher at mcgill.ca  Wed Jun  1 13:44:03 2022
From: xavier.lecoursboucher at mcgill.ca (Xavier Lecours Boucher, Mr)
Date: Wed, 1 Jun 2022 17:44:03 +0000
Subject: [Loris-dev] PHP Fatal error:  Allowed memory size of
In-Reply-To: <AB308F6A-F1C8-4924-A5C5-5E8D3BA87533@bwh.harvard.edu>
References: <AB308F6A-F1C8-4924-A5C5-5E8D3BA87533@bwh.harvard.edu>
Message-ID: <QB1PR01MB2356D4C890E054EDF7D899EDFCDF9@QB1PR01MB2356.CANPRD01.PROD.OUTLOOK.COM>

Hi Alfredo,

Are you running LORIS 22?
I am asking because LORIS 23 added the following at the end of index.php:


// Include the body.
$bodystream = $response->getBody();

// First we need to disable any output buffering so that
// it streams to the output instead of into the buffer
// and uses up all the memory for large chunks of data.
for ($i = ob_get_level(); $i != 0; $i = ob_get_level()) {
    ob_end_clean();
}
ob_implicit_flush();

while ($bodystream->eof() == false) {
    // 64k oughta be enough for anybody.
    print $bodystream->read(1024*64);
}

Try adding those lines if they are not there. Let us know if the issue persists.

-  Xavier Lecours


________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca <loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU>
Sent: May 31, 2022 3:53 PM
To: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
Cc: Vladimir S. FONOV <v.s.fonov at ilmarin.info>; Sridar Narayanan, Dr. <sridar.narayanan at mcgill.ca>; Guttmann, Charles, M.D. <guttmann at bwh.harvard.edu>
Subject: [Loris-dev] PHP Fatal error: Allowed memory size of

Dear LorisDev team,

I?m facing the following error when downloading a large minc image (~70MB) using the API ?GET /candidates/$CandID/$VisitLabel/images/$Filename?. I can download the file from the web interface with no issues.

===
[Tue May 31 15:25:10.697608 2022] [php7:error] [pid 20168] [client 73.219.242.88:64779] PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 70594560 bytes) in /var/www/loris/htdocs/index.php on line 63
===

I googled the error but couldn?t find a solution, do you know how fix this?

Best regards,
Alfredo.
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 https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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From AMORALESPINZON at BWH.HARVARD.EDU  Mon Jun  6 13:33:10 2022
From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo)
Date: Mon, 6 Jun 2022 17:33:10 +0000
Subject: [Loris-dev] PHP Fatal error:  Allowed memory size of
In-Reply-To: <QB1PR01MB2356D4C890E054EDF7D899EDFCDF9@QB1PR01MB2356.CANPRD01.PROD.OUTLOOK.COM>
References: <AB308F6A-F1C8-4924-A5C5-5E8D3BA87533@bwh.harvard.edu>
 <QB1PR01MB2356D4C890E054EDF7D899EDFCDF9@QB1PR01MB2356.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <3DB18C03-7052-4127-BABF-1FAF86F6E036@bwh.harvard.edu>

Hi Xavier,

Thank you, now it?s working. I?m running LORIS 23.0.2.

I struggled a little cause I didn?t know if the line ?print $response->getBody();?  was supposed to be replaced or not. After testing I figured out it has to be replaced, otherwise I cannot even get a token.

Best,
Alfredo.

On Jun 1, 2022, at 1:44 PM, Xavier Lecours Boucher, Mr <xavier.lecoursboucher at mcgill.ca<mailto:xavier.lecoursboucher at mcgill.ca>> wrote:

        External Email - Use Caution

Hi Alfredo,

Are you running LORIS 22?
I am asking because LORIS 23 added the following at the end of index.php:


// Include the body.
$bodystream = $response->getBody();

// First we need to disable any output buffering so that
// it streams to the output instead of into the buffer
// and uses up all the memory for large chunks of data.
for ($i = ob_get_level(); $i != 0; $i = ob_get_level()) {
    ob_end_clean();
}
ob_implicit_flush();

while ($bodystream->eof() == false) {
    // 64k oughta be enough for anybody.
    print $bodystream->read(1024*64);
}

Try adding those lines if they are not there. Let us know if the issue persists.

-  Xavier Lecours


________________________________
From: loris-dev-bounces at bic.mni.mcgill.ca<mailto:loris-dev-bounces at bic.mni.mcgill.ca> <loris-dev-bounces at bic.mni.mcgill.ca<mailto:loris-dev-bounces at bic.mni.mcgill.ca>> on behalf of Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.EDU>>
Sent: May 31, 2022 3:53 PM
To: loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca> <loris-dev at bic.mni.mcgill.ca<mailto:loris-dev at bic.mni.mcgill.ca>>
Cc: Vladimir S. FONOV <v.s.fonov at ilmarin.info<mailto:v.s.fonov at ilmarin.info>>; Sridar Narayanan, Dr. <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>>; Guttmann, Charles, M.D. <guttmann at bwh.harvard.edu<mailto:guttmann at bwh.harvard.edu>>
Subject: [Loris-dev] PHP Fatal error: Allowed memory size of

Dear LorisDev team,

I?m facing the following error when downloading a large minc image (~70MB) using the API ?GET /candidates/$CandID/$VisitLabel/images/$Filename?. I can download the file from the web interface with no issues.

===
[Tue May 31 15:25:10.697608 2022] [php7:error] [pid 20168] [client 73.219.242.88:64779] PHP Fatal error:  Allowed memory size of 134217728 bytes exhausted (tried to allocate 70594560 bytes) in /var/www/loris/htdocs/index.php on line 63
===

I googled the error but couldn?t find a solution, do you know how fix this?

Best regards,
Alfredo.
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 https://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/19Xn1xkn4b3-sRGHnfX12KxJD_v-e0qwKTzXYxPYWXqoWcX-GJKFEPdgPQdtrGREi9fmjt0ksBKSqe66_VjQccu0NQPWjBxOqEwj8KFxpvlnHE_4bHa9aPT-GEHg6GwUS3zirAQAW9tUIsObknMn6uE2t28Hzmsxb9s6qvPgZehpoZ3leS8GkaQPNbEErNQcqAOZv0xHywYT9PvJpWm7QyaYJ9guZxDC57fFqsqVXJ1t6aq2s6G88SMuDysPHUT2ClssKO2rfLHm-vJkuQHUI5KcJO8W2vK1vd4zoecHI5D76VeygSHlsPIZdSTd90XWCl_ce_WaY-UaNlP2WnGD6sg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline><https://www.massgeneralbrigham.org/complianceline<https://secure-web.cisco.com/19Xn1xkn4b3-sRGHnfX12KxJD_v-e0qwKTzXYxPYWXqoWcX-GJKFEPdgPQdtrGREi9fmjt0ksBKSqe66_VjQccu0NQPWjBxOqEwj8KFxpvlnHE_4bHa9aPT-GEHg6GwUS3zirAQAW9tUIsObknMn6uE2t28Hzmsxb9s6qvPgZehpoZ3leS8GkaQPNbEErNQcqAOZv0xHywYT9PvJpWm7QyaYJ9guZxDC57fFqsqVXJ1t6aq2s6G88SMuDysPHUT2ClssKO2rfLHm-vJkuQHUI5KcJO8W2vK1vd4zoecHI5D76VeygSHlsPIZdSTd90XWCl_ce_WaY-UaNlP2WnGD6sg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca<mailto:Loris-dev at bic.mni.mcgill.ca>
https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev<https://secure-web.cisco.com/1SRATtcJN8mR3gVYhf8wjH6_Novm6aJ3dARF2iUwiswpC92wu1AtsyGLwir5GQk5R84IA3r6JavmDpqUzwL_sauPcOoVayH8E5SRGuuz4NJvl71mpJZFn1hYK82mYlScvdBCz-MqqFTGbbEmh1QeIT4Tzxu7HRm9esC-CLf1KYsoZ9MVdX_bcijR8ti0vVk74k6mVIrqRHGvf2hKlENITA1GEj_I_ogovktBMxtRydH3A_RcfBF5H_4tKjF1Kje2S_7-txcQktszdEWcyh0ayVJM93u8NspqcYO8ivgMQXYuaWHyBM0qeEHgweMeCInU9R7DQiRQk5lcdy54rRdviUw/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev>

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 https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 
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From molano at ext.cnio.es  Tue Jun  7 08:44:58 2022
From: molano at ext.cnio.es (=?iso-8859-1?Q?Olano=2EMar=EDa?=)
Date: Tue, 7 Jun 2022 12:44:58 +0000
Subject: [Loris-dev] .czi image upload
Message-ID: <1AAB0BC03205B240B7809934CFCF8DF52E2B22@DONAR.cnio.es>

Good day,

We were hoping to use LORIS as a way to upload .czi pathology images onto the plataform; however, it seems only DICOM MRI images can be uploaded. Is there a way of importing .czi images?  Would the Imaging Uploader front end on the LORIS web plataform still function with .czi?


Thank you

Mar?a




[Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer] <https://www.cnio.es/es/colaborar/comocolaborar.asp>

Fb Amigos del CNIO<https://www.facebook.com/AmigosdelCNIO/> |  Tw @CNIOStopCancer<https://twitter.com/CNIOStopCancer> |  Youtube canalcnio<https://www.youtube.com/canalcnio>


**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp
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From christine.rogers at mcgill.ca  Tue Jun  7 09:20:15 2022
From: christine.rogers at mcgill.ca (Christine Rogers, Ms.)
Date: Tue, 7 Jun 2022 13:20:15 +0000
Subject: [Loris-dev] .czi image upload
In-Reply-To: <1AAB0BC03205B240B7809934CFCF8DF52E2B22@DONAR.cnio.es>
References: <1AAB0BC03205B240B7809934CFCF8DF52E2B22@DONAR.cnio.es>
Message-ID: <BF352BF3-84CD-4EA8-AEDA-471E2E43F9B7@mcgill.ca>

Hello,
Thanks for your question ?
 LORIS?s open-source imaging pipelines support DICOM, MINC and NIFTI, and can be customized for different technologies, standards, and domain-specific standards.
For proprietary formats like .CZI in microscopy, you may wish to use community-supported converters(*) to DICOM.

Customizing LORIS may also be an option for your project? modifying code in the pipelines and open-source database and web-facing workflows for your chosen format.  You could then potentially use either the imaging pipelines or the Imaging Uploader to import .czi
Best,
Christine

* e.g. this open-source toolkit would support .CZI to DICOM conversion:
http://dx.doi.org/10.1109/ISCC53001.2021.9631529

On Jun 7, 2022, at 8:45 AM, Olano.Mar?a <molano at ext.cnio.es> wrote:

?
Good day,

We were hoping to use LORIS as a way to upload .czi pathology images onto the plataform; however, it seems only DICOM MRI images can be uploaded. Is there a way of importing .czi images?  Would the Imaging Uploader front end on the LORIS web plataform still function with .czi?


Thank you

Mar?a




[Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer] <https://www.cnio.es/es/colaborar/comocolaborar.asp>

Fb Amigos del CNIO<https://www.facebook.com/AmigosdelCNIO/> |  Tw @CNIOStopCancer<https://twitter.com/CNIOStopCancer> |  Youtube canalcnio<https://www.youtube.com/canalcnio>


**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp _______________________________________________
Loris-dev mailing list
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From tikal004 at umn.edu  Fri Jun 17 11:02:21 2022
From: tikal004 at umn.edu (Barry Tikalsky)
Date: Fri, 17 Jun 2022 10:02:21 -0500
Subject: [Loris-dev] Data Query Tool error
Message-ID: <CAJoAM3mmGHx-q2+qmD2MO71jht5=QFDnmCkS5XXaPbF_J8UcMQ@mail.gmail.com>

Hello Loris Devs,

When running the data query tool we consistently see no data returned. It
was working a week ago, but something seems to have changed.
The following is from the php error log, it leads me to believe there are
permissions errors somewhere. Where is the temp file created? What
configuration setting might lead to this permissions issue?
Thanks!

[Thu Jun 16 12:23:35.037463 2022] [php7:notice] [pid 32400] [client
10.32.130.238:61581] PHP Notice:  Unknown: file created in the system's
temporary directory in Unknown on line 0, referer:
https://elab.ahc.umn.edu/dataquery/
[Thu Jun 16 12:23:35.037544 2022] [php7:warn] [pid 32400] [client
10.32.130.238:61581] PHP Warning:  Unknown: Unable to create temporary
file, Check permissions in temporary files directory. in Unknown on line 0,
referer: https://elab.ahc.umn.edu/dataquery/
[Thu Jun 16 12:23:35.037554 2022] [php7:warn] [pid 32400] [client
10.32.130.238:61581] PHP Warning:  Unknown: POST data can't be buffered;
all data discarded in Unknown on line 0, referer:
https://elab.ahc.umn.edu/dataquery/
[Thu Jun 16 12:23:35.169173 2022] [php7:notice] [pid 32400] [client
10.32.130.238:61581] PHP Notice:  Undefined index: DocType in
/swadm/var/www/elab_loris/modules/dataquery/ajax/retrieveCategoryDocs.php
on line 34, referer: https://elab.ahc.umn.edu/dataquery/
[Thu Jun 16 12:23:35.169230 2022] [php7:notice] [pid 32400] [client
10.32.130.238:61581] PHP Notice:  Undefined index: Sessions in
/swadm/var/www/elab_loris/modules/dataquery/ajax/retrieveCategoryDocs.php
on line 35, referer: https://elab.ahc.umn.edu/dataquery/
[Thu Jun 16 12:23:35.169251 2022] [php7:warn] [pid 32400] [client
10.32.130.238:61581] PHP Warning:  array_map(): Expected parameter 2 to be
an array, null given in
/swadm/var/www/elab_loris/modules/dataquery/ajax/retrieveCategoryDocs.php
on line 40, referer: https://elab.ahc.umn.edu/dataquery/
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From molano at ext.cnio.es  Mon Jun 20 04:04:43 2022
From: molano at ext.cnio.es (=?iso-8859-1?Q?Olano=2EMar=EDa?=)
Date: Mon, 20 Jun 2022 08:04:43 +0000
Subject: [Loris-dev] Follow up czi question
Message-ID: <1AAB0BC03205B240B7809934CFCF8DF52E2E69@DONAR.cnio.es>

Hello,

Unfortunately, we can't change the initial format (.CZI) to DICOM,so our next option is to customizing loris by modifying code in the pipelines and open-source database and web-facing workflows. In previous emails with Olga Rico, your team recommended importing them using your Derived Data script (even though this is raw data).

We would like to have a better understanding of how to modify loris' code in order to carry out .czi uploads. Any indication of where to start would be very much appreciated.
Thank you,
Mar?a





[Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer] <https://www.cnio.es/es/colaborar/comocolaborar.asp>

Fb Amigos del CNIO<https://www.facebook.com/AmigosdelCNIO/> |  Tw @CNIOStopCancer<https://twitter.com/CNIOStopCancer> |  Youtube canalcnio<https://www.youtube.com/canalcnio>


**ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a la protecci?n de los datos personales de las personas f?sicas, la informaci?n personal que nos pueda facilitar a trav?s de este correo electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de tramitar el objeto del presente correo electr?nico. El tratamiento de sus datos personales se encuentra legitimado por ser necesario para gestionar el objeto del presente mensaje. Estos datos personales no ser?n comunicados a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga exigido por una ley. Ud. podr? ejercer los derechos de acceso, rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029 (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer informaci?n adicional sobre el tratamiento de sus datos personales, puede consultar dicha informaci?n adicional en el siguiente enlace dentro de nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp

**LEGAL NOTICE**: This email and any attached files may contain protected information for the sole use of its intended recipient or addressee. Anyone other than the intended recipient or addressee is strictly prohibited from distributing, reproducing or transmitting the email and its contents in any way. If you receive this email in error, please notify the sender and delete the message.
Pursuant to the provisions of EU Regulation 2016/679 regarding the protection of personal data, any personal information you provide through this email will be registered by the CNIO Foundation in order to deal with content of this email. Your personal data must be processed in order to be able to deal with the content and purpose of this message. Your personal details will not be passed on to anyone else unless you authorise us to do so or we are required to do so by law. You may exercise your rights regarding access, rectification, suppression, limitation of processing, portability and opposition by writing to the following address: c/Melchor Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If you require further information about the processing of your personal data, go to the following link on our webpage: https://www.cnio.es/es/privacidad/index.asp
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From rogers at bic.mni.mcgill.ca  Mon Jun 20 12:19:40 2022
From: rogers at bic.mni.mcgill.ca (Christine Rogers)
Date: Mon, 20 Jun 2022 17:19:40 +0100
Subject: [Loris-dev] .czi image upload
In-Reply-To: <ba1f83a878704977ae5103c839a48722@YQBPR0101MB4211.CANPRD01.PROD.OUTLOOK.COM>
References: <1AAB0BC03205B240B7809934CFCF8DF52E2B22@DONAR.cnio.es>
 <BF352BF3-84CD-4EA8-AEDA-471E2E43F9B7@mcgill.ca>
 <ba1f83a878704977ae5103c839a48722@YQBPR0101MB4211.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <CALbt7NCjuCQAqfLSSPYPhCyeXrYV9c3F1uLq3zOvOZFFo45RVw@mail.gmail.com>

Hi Maria,
Sure, all our documentation on how the pipelines work and how you might
approach modifying them is available in the LORIS-MRI repository (
github.com/aces/loris-mri) under the docs/ folder.
You may wish to start here:
https://github.com/aces/Loris-MRI/blob/main/docs/01-Introduction.md
Let us know what your followup questions might be based on this
information, and we'll be glad to get back to you.
Best,
Christine



On Wed, Jun 15, 2022 at 2:35 PM Olano.Mar?a <molano at ext.cnio.es> wrote:

> Hello,
>
>
>
> Unfortunately, we can?t change the initial format (.CZI) to DICOM,so our
> next option is to customizing loris by modifying code in the pipelines
> and open-source database and web-facing workflows. In previous emails with
> Olga Rico, your team recommended importing them using your Derived Data
> script (even though this is raw data).
>
>
>
> We would like to have a better understanding of how to modify loris? code
> in order to carry out .czi uploads. Any indication of where to start would
> be very much appreciated.
>
> Thank you,
>
> Mar?a
>
>
>
> *De:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>
> *Enviado el:* martes, 7 de junio de 2022 15:20
> *Para:* Olano.Mar?a <molano at ext.cnio.es>
> *CC:* loris-dev at bic.mni.mcgill.ca
> *Asunto:* Re: [Loris-dev] .czi image upload
>
>
>
> *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*
>
>
>
> Hello,
>
> Thanks for your question ?
>
>  LORIS?s open-source imaging pipelines support DICOM, MINC and NIFTI, and
> can be customized for different technologies, standards, and
> domain-specific standards.
>
> For proprietary formats like .CZI in microscopy, you may wish to use
> community-supported converters(*) to DICOM.
>
>
>
> Customizing LORIS may also be an option for your project? modifying code
> in the pipelines and open-source database and web-facing workflows for your
> chosen format.  You could then potentially use either the imaging pipelines
> or the Imaging Uploader to import .czi
>
> Best,
>
> Christine
>
>
>
> * e.g. this open-source toolkit would support .CZI to DICOM conversion:
>
> http://dx.doi.org/10.1109/ISCC53001.2021.9631529
>
>
>
> On Jun 7, 2022, at 8:45 AM, Olano.Mar?a <molano at ext.cnio.es> wrote:
>
> ?
>
> Good day,
>
>
>
> We were hoping to use LORIS as a way to upload .czi pathology images onto
> the plataform; however, it seems only DICOM MRI images can be uploaded. Is
> there a way of importing .czi images?  Would the Imaging Uploader front end
> on the LORIS web plataform still function with .czi?
>
>
>
>
>
> Thank you
>
>
>
> Mar?a
>
>
>
> [image: Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer]
> <https://www.cnio.es/es/colaborar/comocolaborar.asp>
>
> *Fb* Amigos del CNIO <https://www.facebook.com/AmigosdelCNIO/> |  *Tw*
> @CNIOStopCancer <https://twitter.com/CNIOStopCancer> |  *Youtube*
> canalcnio <https://www.youtube.com/canalcnio>
>
>
>
> **ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros
> adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su
> destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro
> tipo de transmisi?n por parte de otra persona que no sea el destinatario.
> Si usted recibe por error este correo, se ruega comunicarlo al remitente y
> borrar el mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a
> la protecci?n de los datos personales de las personas f?sicas, la
> informaci?n personal que nos pueda facilitar a trav?s de este correo
> electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de
> tramitar el objeto del presente correo electr?nico. El tratamiento de sus
> datos personales se encuentra legitimado por ser necesario para gestionar
> el objeto del presente mensaje. Estos datos personales no ser?n comunicados
> a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga
> exigido por una ley. Ud. podr? ejercer los derechos de acceso,
> rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y
> oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029
> (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos
> en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer
> informaci?n adicional sobre el tratamiento de sus datos personales, puede
> consultar dicha informaci?n adicional en el siguiente enlace dentro de
> nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp
>
> **LEGAL NOTICE**: This email and any attached files may contain protected
> information for the sole use of its intended recipient or addressee. Anyone
> other than the intended recipient or addressee is strictly prohibited from
> distributing, reproducing or transmitting the email and its contents in any
> way. If you receive this email in error, please notify the sender and
> delete the message.
> Pursuant to the provisions of EU Regulation 2016/679 regarding the
> protection of personal data, any personal information you provide through
> this email will be registered by the CNIO Foundation in order to deal with
> content of this email. Your personal data must be processed in order to be
> able to deal with the content and purpose of this message. Your personal
> details will not be passed on to anyone else unless you authorise us to do
> so or we are required to do so by law. You may exercise your rights
> regarding access, rectification, suppression, limitation of processing,
> portability and opposition by writing to the following address: c/Melchor
> Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection
> Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If
> you require further information about the processing of your personal data,
> go to the following link on our webpage:
> https://www.cnio.es/es/privacidad/index.asp
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>
>
> **ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros
> adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su
> destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro
> tipo de transmisi?n por parte de otra persona que no sea el destinatario.
> Si usted recibe por error este correo, se ruega comunicarlo al remitente y
> borrar el mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a
> la protecci?n de los datos personales de las personas f?sicas, la
> informaci?n personal que nos pueda facilitar a trav?s de este correo
> electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de
> tramitar el objeto del presente correo electr?nico. El tratamiento de sus
> datos personales se encuentra legitimado por ser necesario para gestionar
> el objeto del presente mensaje. Estos datos personales no ser?n comunicados
> a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga
> exigido por una ley. Ud. podr? ejercer los derechos de acceso,
> rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y
> oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029
> (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos
> en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer
> informaci?n adicional sobre el tratamiento de sus datos personales, puede
> consultar dicha informaci?n adicional en el siguiente enlace dentro de
> nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp
>
> **LEGAL NOTICE**: This email and any attached files may contain protected
> information for the sole use of its intended recipient or addressee. Anyone
> other than the intended recipient or addressee is strictly prohibited from
> distributing, reproducing or transmitting the email and its contents in any
> way. If you receive this email in error, please notify the sender and
> delete the message.
> Pursuant to the provisions of EU Regulation 2016/679 regarding the
> protection of personal data, any personal information you provide through
> this email will be registered by the CNIO Foundation in order to deal with
> content of this email. Your personal data must be processed in order to be
> able to deal with the content and purpose of this message. Your personal
> details will not be passed on to anyone else unless you authorise us to do
> so or we are required to do so by law. You may exercise your rights
> regarding access, rectification, suppression, limitation of processing,
> portability and opposition by writing to the following address: c/Melchor
> Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection
> Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If
> you require further information about the processing of your personal data,
> go to the following link on our webpage:
> https://www.cnio.es/es/privacidad/index.asp
>


-- 
Research Project Officer
christine.rogers at mcgill.ca
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute-Hospital
McGill University | Montreal | Canada
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From cecile.madjar at mcin.ca  Mon Jun 20 13:38:42 2022
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 20 Jun 2022 13:38:42 -0400
Subject: [Loris-dev] Follow up czi question
In-Reply-To: <1AAB0BC03205B240B7809934CFCF8DF52E2E69@DONAR.cnio.es>
References: <1AAB0BC03205B240B7809934CFCF8DF52E2E69@DONAR.cnio.es>
Message-ID: <CAMkiY3cjM-JpKJXbSZ4VYeNaGTT-JouUf=HRCpyLnFjGVs+K+g@mail.gmail.com>

Hello Maria,

I may be wrong but I think you could use some already existing scripts to
do what you need. Here what you most likely to do to adapt LORIS for czi
files:

   - zip the .czi files of a given session together with PatientName like
   looks like "PSCID_CandID_VisitLabel" and upload the file in the imaging
   uploader
   - set up a cronjob that would unzip the archive containing the .czi
   files and use imaging_non_minc_insertion.pl
   <https://github.com/aces/Loris-MRI/blob/main/uploadNeuroDB/imaging_non_minc_insertion.pl>
script
   to insert the files into the imaging browser

One caveat: I don't think BrainBrowser will be able to view the images like
MINC or NIfTI files but at least, the data will be properly organized in
the database.

There might need some tweaking along the way but it should be feasible.

Hope this helps,

C?cile

On Mon, Jun 20, 2022 at 4:05 AM Olano.Mar?a <molano at ext.cnio.es> wrote:

> Hello,
>
>
>
> Unfortunately, we can?t change the initial format (.CZI) to DICOM,so our
> next option is to customizing loris by modifying code in the pipelines
> and open-source database and web-facing workflows. In previous emails with
> Olga Rico, your team recommended importing them using your Derived Data
> script (even though this is raw data).
>
>
>
> We would like to have a better understanding of how to modify loris? code
> in order to carry out .czi uploads. Any indication of where to start would
> be very much appreciated.
>
> Thank you,
>
> Mar?a
>
>
>
>
>
> [image: Hazte Amigo del CNIO. M?s investigaci?n, menos c?ncer]
> <https://www.cnio.es/es/colaborar/comocolaborar.asp>
>
> *Fb* Amigos del CNIO <https://www.facebook.com/AmigosdelCNIO/> |  *Tw*
> @CNIOStopCancer <https://twitter.com/CNIOStopCancer> |  *Youtube*
> canalcnio <https://www.youtube.com/canalcnio>
>
>
> **ADVERTENCIA LEGAL**: Este correo electr?nico, y en su caso los ficheros
> adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su
> destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro
> tipo de transmisi?n por parte de otra persona que no sea el destinatario.
> Si usted recibe por error este correo, se ruega comunicarlo al remitente y
> borrar el mensaje recibido.
> De conformidad con lo dispuesto en el Reglamento (UE) 2016/679 relativo a
> la protecci?n de los datos personales de las personas f?sicas, la
> informaci?n personal que nos pueda facilitar a trav?s de este correo
> electr?nico quedar? registrada por la Fundaci?n CNIO con la finalidad de
> tramitar el objeto del presente correo electr?nico. El tratamiento de sus
> datos personales se encuentra legitimado por ser necesario para gestionar
> el objeto del presente mensaje. Estos datos personales no ser?n comunicados
> a ning?n destinatario salvo a aquellos que usted nos autorice o as? venga
> exigido por una ley. Ud. podr? ejercer los derechos de acceso,
> rectificaci?n, supresi?n, limitaci?n de tratamiento, portabilidad y
> oposici?n en la siguiente direcci?n: c/Melchor Fernandez Almagro 3, 28029
> (Madrid). Podr? ponerse en contacto con el Delegado de Protecci?n de Datos
> en: delegado_lopd at cnio.es. Para el caso de que Ud. precise conocer
> informaci?n adicional sobre el tratamiento de sus datos personales, puede
> consultar dicha informaci?n adicional en el siguiente enlace dentro de
> nuestra p?gina web: https://www.cnio.es/es/privacidad/index.asp
>
> **LEGAL NOTICE**: This email and any attached files may contain protected
> information for the sole use of its intended recipient or addressee. Anyone
> other than the intended recipient or addressee is strictly prohibited from
> distributing, reproducing or transmitting the email and its contents in any
> way. If you receive this email in error, please notify the sender and
> delete the message.
> Pursuant to the provisions of EU Regulation 2016/679 regarding the
> protection of personal data, any personal information you provide through
> this email will be registered by the CNIO Foundation in order to deal with
> content of this email. Your personal data must be processed in order to be
> able to deal with the content and purpose of this message. Your personal
> details will not be passed on to anyone else unless you authorise us to do
> so or we are required to do so by law. You may exercise your rights
> regarding access, rectification, suppression, limitation of processing,
> portability and opposition by writing to the following address: c/Melchor
> Fernandez Almagro 3, 28029 (Madrid). You may contact the Data Protection
> Delegate (Delegado de Protecci?n de Datos) at: delegado_lopd at cnio.es. If
> you require further information about the processing of your personal data,
> go to the following link on our webpage:
> https://www.cnio.es/es/privacidad/index.asp
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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