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

[Gregory Luneau]

Hi Ganesh, it is good like this:

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

it will add the uploadNeuroDB perl libraries to those already in the
variable $PERL5LIB.




On Wed, Jul 5, 2017 at 8:58 AM, Ganesh Chauhan (CBR) <
ganesh.chauhan at cbr.iisc.ac.in> wrote:

> 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) <
> 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/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
>> +91 80 2293 3009 <+91%2080%202293%203009>
>> https://www.cbr.iisc.ac.in
>>
>> --
>> This message has been scanned for viruses and
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>>
>> _______________________________________________
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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 <+91%2080%202293%203009>
> https://www.cbr.iisc.ac.in
>



-- 

Gregory Luneau

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