[Loris-dev] Pre-processing MRI DICOM files and Insertion into Loris

[Ganesh Chauhan (CBR)]

Dear Gregory, 

I am not sure what should go into the following line in the file environment 

export PERL5LIB=/data/Loris/bin/mri/uploadNeuroDB:$PERL5LIB 

Any suggestions like should it be: 

export PERL5LIB=/usr/share/perl/5.22:$PERL5LIB 


Many thanks. 

With best regards, 
Ganesh 

From: "Gregory Luneau" <gluneau.mcin at gmail.com> 
To: "Ganesh Chauhan, CBR" <ganesh.chauhan at cbr.iisc.ac.in> 
Cc: "loris-dev" <loris-dev at bic.mni.mcgill.ca> 
Sent: Wednesday, July 5, 2017 5:31:15 PM 
Subject: Re: [Loris-dev] Pre-processing MRI DICOM files and Insertion into Loris 

Hello Ganesh, as for processing the image on the command line, you'll need to source the environment file first, like this: 
source /data/Loris/bin/mri/environment 
Take a look at that environment file first and make sure everything seems ok. 

Then as a second step, run the imaging upload script. 

Good day, 


On Wed, Jul 5, 2017 at 7:18 AM, Ganesh Chauhan (CBR) < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] > wrote: 



Dear team Loris, 

I uploaded a zipped file containing DICOM image files via the front end using "Imaging Uploader". The file got uploaded but the "Progress" section in the table displayed "Failure". 
Then I wanted to process the image files through the back end. For which I typed the following command: 

/data/Loris/bin/mri/uploadNeuroDB/ [ http://imaging_upload_file.pl/ | imaging_upload_file.pl ] /data/incoming/CBR035_734440_V1.zip -upload_id 3 -profile prod 

I got the error message: 

ERROR: You don't have a 
configuration file named 'prod' in: 
/data/Loris/bin/mri/dicom-archive/.loris_mri/ 

Since I am sure I have this file in the desired location and I can view the configuration file called "prod", I do not understand why I get this error. 

Your help is highly appreciated. 

With best regards, 
Ganesh 


-- 
Ganesh Chauhan (PhD) 
Scientist 
Centre for Brain Research (CBR) 
Indian Institute of Science (IISc) 
Bengaluru, INDIA 
[ tel:+91%2080%202293%203009 | +91 80 2293 3009 ] 
[ https://www.cbr.iisc.ac.in/ | https://www.cbr.iisc.ac.in ] 

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-- 

Gregory Luneau 

McGill Centre for Integrative Neuroscience (MCIN), 
Ludmer Centre for Neuroinformatics and Mental Health, 
Montreal Neurological Institute (MNI), 
McGill University, Montreal, Canada 


-- 
Ganesh Chauhan (PhD) 
Scientist 
Centre for Brain Research (CBR) 
Indian Institute of Science (IISc) 
Bengaluru, INDIA 
+91 80 2293 3009 
https://www.cbr.iisc.ac.in 
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