[Loris-dev] Import mri - scripts

Wed Sep 4 10:35:56 EDT 2019

Hi Sotirios,

Ok, this sounds like good progress.  Let us know when you next encounter issues as you progress through the Imaging Install/Setup docs<https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md>.
I'll look into how we can better handle the incoming/ directory next time.
Best,
Christine

On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
/data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is populated correctly except its port is  'port'    : ''. Also i have tested that i can connect to MySQL with lorisuser.

I executed the script again, because the only error i had previously was that the /data/incoming folder didn't exist and there are no errors reported back except of warnings <<mysql: [Warning] Using a password on the command line interface can be insecure>>.

Στις Τετ, 4 Σεπ 2019 στις 4:53 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> έγραψε:
Hi Sotirios,

It's possible -- if the script was unable to connect to the database during its execution (e.g. typo in the password), that would explain the underpopulated Image path and Loris-MRI code path you saw in the Config module.
It's hard to tell without seeing the output from your script run -- Did you see a sign of any such error?
The Config fields are populated by the imaging_install.sh script (starting at line 222<https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222>)

For example, check if the database connection information was populated accurately in $mridir/dicom-archive/.loris_mri/database_config.py

Best,
Christine

On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
Hi Christine,

If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically?

Thanks

[https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs]

Στις Τετ, 4 Σεπ 2019 στις 4:16 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> έγραψε:
Hi Sotirios,

Glad to hear your LORIS core install is up and working and all the front-end pages are loading.

> lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project
> and the web interface worked.

Yes, it's important that project/ have 775 permissions and that lorisadmin be part of the sudoers group, per step 1 in the install Readme<https://github.com/aces/Loris#install-steps>.

> As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right?

These imaging paths will be updated during your imaging installation<https://github.com/aces/Loris/wiki/Setup> by an automated script -- you do not need to set them manually via the Config module.
Please continue to follow the Setup Guide<https://github.com/aces/Loris/wiki/Setup> for detailed steps to follow.

Best,
Christine

On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right?

[image.png]

Στις Τετ, 4 Σεπ 2019 στις 2:28 μ.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> έγραψε:
Hi,

i used

curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash -
sudo apt-get install -y nodejs

you had suggested in the past, make worked and now i can see all the contents in the web-interface, but i don't need make install?

Thanks
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christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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