From asl1 at ualberta.ca  Thu Nov  5 15:13:50 2015
From: asl1 at ualberta.ca (Angela Lee)
Date: Thu, 5 Nov 2015 13:13:50 -0700
Subject: [Loris-dev] LORIS - installation difficulties
Message-ID: <CAJERcg2enbVWHBG09FfNB+_6dn73xhQx23ZtJWBun1Z6QNMbtg@mail.gmail.com>

Hi,

I'm currently trying to install LORIS on a virtual machine to see our lab
would like to use it for an upcoming project. I'm having difficulty with
running the installation script. I keep getting the message "Could not
create the database with the root user provided".

Thanks,
-- 
Angela Lee, Hon. BA&Sc, Student Research Assistant
Department of Medicine - Neurology
University of Alberta

*Email:* asl1 at ualberta.ca
*Phone: *1-(780)-248-1943
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From christine.rogers at mcgill.ca  Fri Nov  6 17:52:07 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Fri, 6 Nov 2015 17:52:07 -0500
Subject: [Loris-dev] LORIS - installation difficulties
In-Reply-To: <CAJERcg2enbVWHBG09FfNB+_6dn73xhQx23ZtJWBun1Z6QNMbtg@mail.gmail.com>
References: <CAJERcg2enbVWHBG09FfNB+_6dn73xhQx23ZtJWBun1Z6QNMbtg@mail.gmail.com>
Message-ID: <CALbt7NDWQjTq=UJDnv4rb4YGcUYoRFRWsd3q=iSBQn8QSC6Nwg@mail.gmail.com>

Hi Angela,
Thanks for your question.
While running the Install script, if you are encountering the message "Could
not create the database with the root user provided"  it's most likely
because the username and password you are providing doesn't have permission
to create a database on the MySQL service you are logging into.
Are you using the "root" user credential?  If so, some other issue may be
the cause - feel free to let us know if you have further questions.

Specifically, the privilege CREATE_DATABASE is required to create a new
database in MySQL.  If you have been granted a non-root user account to log
into mysql hosted elsewhere (on a different server or VM), then the
administrator who gave you the account can create a blank database for you
(e.g. called "loris"), which the install script can then automatically
populate for you based on the default schema.

Best,
Christine


On Thu, Nov 5, 2015 at 3:13 PM, Angela Lee <asl1 at ualberta.ca> wrote:

> Hi,
>
> I'm currently trying to install LORIS on a virtual machine to see our lab
> would like to use it for an upcoming project. I'm having difficulty with
> running the installation script. I keep getting the message "Could not
> create the database with the root user provided".
>
> Thanks,
> --
> Angela Lee, Hon. BA&Sc, Student Research Assistant
> Department of Medicine - Neurology
> University of Alberta
>
> *Email:* asl1 at ualberta.ca
> *Phone: *1-(780)-248-1943
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>


-- 

christine.rogers at mcgill.ca
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada
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From asl1 at ualberta.ca  Mon Nov  9 16:59:28 2015
From: asl1 at ualberta.ca (Angela Lee)
Date: Mon, 9 Nov 2015 14:59:28 -0700
Subject: [Loris-dev] LORIS - installation difficulties
In-Reply-To: <CALbt7NDWQjTq=UJDnv4rb4YGcUYoRFRWsd3q=iSBQn8QSC6Nwg@mail.gmail.com>
References: <CAJERcg2enbVWHBG09FfNB+_6dn73xhQx23ZtJWBun1Z6QNMbtg@mail.gmail.com>
	<CALbt7NDWQjTq=UJDnv4rb4YGcUYoRFRWsd3q=iSBQn8QSC6Nwg@mail.gmail.com>
Message-ID: <CAJERcg3cDSx6O09yPqjdiVwxvNYm5ydF7QgCXpLdxSC4e-30kw@mail.gmail.com>

Hi Christine,

thanks for your help. I was able to create the database. Now, I'm wondering
how I would be able to make this accessible via the internet for the other
sites that would be involved in our study. Would I need to set up a new
hostname and register a domain name? I am also not too sure how to go about
doing that.

Thanks for all your help,
Angela

On Fri, Nov 6, 2015 at 3:52 PM, Christine Rogers <christine.rogers at mcgill.ca
> wrote:

> Hi Angela,
> Thanks for your question.
> While running the Install script, if you are encountering the message "Could
> not create the database with the root user provided"  it's most likely
> because the username and password you are providing doesn't have permission
> to create a database on the MySQL service you are logging into.
> Are you using the "root" user credential?  If so, some other issue may be
> the cause - feel free to let us know if you have further questions.
>
> Specifically, the privilege CREATE_DATABASE is required to create a new
> database in MySQL.  If you have been granted a non-root user account to log
> into mysql hosted elsewhere (on a different server or VM), then the
> administrator who gave you the account can create a blank database for you
> (e.g. called "loris"), which the install script can then automatically
> populate for you based on the default schema.
>
> Best,
> Christine
>
>
> On Thu, Nov 5, 2015 at 3:13 PM, Angela Lee <asl1 at ualberta.ca> wrote:
>
>> Hi,
>>
>> I'm currently trying to install LORIS on a virtual machine to see our lab
>> would like to use it for an upcoming project. I'm having difficulty with
>> running the installation script. I keep getting the message "Could not
>> create the database with the root user provided".
>>
>> Thanks,
>> --
>> Angela Lee, Hon. BA&Sc, Student Research Assistant
>> Department of Medicine - Neurology
>> University of Alberta
>>
>> *Email:* asl1 at ualberta.ca
>> *Phone: *1-(780)-248-1943
>>
>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>>
>
>
> --
>
> christine.rogers at mcgill.ca
> LORIS data systems | loris.ca
> McGill Centre for Integrative Neuroscience| MCIN.ca
> McConnell Brain Imaging Centre
> Montreal Neurological Institute
> McGill University | Montreal | Canada
>



-- 
Angela Lee, Hon. BA&Sc, Student Research Assistant
Department of Medicine - Neurology
University of Alberta

*Email:* asl1 at ualberta.ca
*Phone: *1-(780)-248-1943
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From najmeh.khalilimahani at mcgill.ca  Tue Nov 10 09:49:50 2015
From: najmeh.khalilimahani at mcgill.ca (Najmeh Khalili-Mahani, Dr)
Date: Tue, 10 Nov 2015 09:49:50 -0500
Subject: [Loris-dev] A question re MRI tables
Message-ID: <CAEpfQgLSghpPznFpfyw5isQQP9VgBpjcR_j9PaqhP0Wn5sirtw@mail.gmail.com>

Hi,

If I understand correctly, before starting to load the MRI data via Image
Uploader, one must manually populate tables with information about the
acquisition times of different sequences (T1, T2, TR, etc.)

This is perhaps a naive question, but I wonder, might it be feasible for
LORIS to have a PERL script that extracts those information from the DICOM
or MINC headers and stores them without human intervention?

Much thanks
Naj

==================================
Najmeh Khalili-Mahani, PhD
Research Associate
McGill Centre for Integrative Neuroscience
Montreal Neurological Institute
McGill University

NW-143, 3801 University St.
Montreal, QC, H3A 2B4
Office: 514-398-1799
email: najma at bic.mni.mcgill.ca
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From christine.rogers at mcgill.ca  Tue Nov 10 16:57:07 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Tue, 10 Nov 2015 16:57:07 -0500
Subject: [Loris-dev] LORIS - installation difficulties
In-Reply-To: <18812_1447106371_56411743_18812_38_38_e294ffc3cdca45eea7187881a82531f1@EXHUB2010-3.campus.MCGILL.CA>
References: <CAJERcg2enbVWHBG09FfNB+_6dn73xhQx23ZtJWBun1Z6QNMbtg@mail.gmail.com>
	<CALbt7NDWQjTq=UJDnv4rb4YGcUYoRFRWsd3q=iSBQn8QSC6Nwg@mail.gmail.com>
	<18812_1447106371_56411743_18812_38_38_e294ffc3cdca45eea7187881a82531f1@EXHUB2010-3.campus.MCGILL.CA>
Message-ID: <CALbt7NB7oSGB58kOJyPi2fLrk=Ri0W6Yp9sP_YYxLP7aWGRgDg@mail.gmail.com>

Hi Angela,
Depending on your network context, a hostname and DNS would enable you to
make your Loris accessible to connections from other sites.  There are also
network-specific configurations that may be possible depending on your
institutional situation.  A sysadmin at your institution or other technical
consultant would be able to provide you with more information on how to
best set this up.
Feel free to let me know if there are further details I could help provide.
Best,
Christine

On Mon, Nov 9, 2015 at 4:59 PM, Angela Lee <asl1 at ualberta.ca> wrote:

> Hi Christine,
>
> thanks for your help. I was able to create the database. Now, I'm
> wondering how I would be able to make this accessible via the internet for
> the other sites that would be involved in our study. Would I need to set up
> a new hostname and register a domain name? I am also not too sure how to go
> about doing that.
>
> Thanks for all your help,
> Angela
>
> On Fri, Nov 6, 2015 at 3:52 PM, Christine Rogers <
> christine.rogers at mcgill.ca> wrote:
>
>> Hi Angela,
>> Thanks for your question.
>> While running the Install script, if you are encountering the message "Could
>> not create the database with the root user provided"  it's most likely
>> because the username and password you are providing doesn't have permission
>> to create a database on the MySQL service you are logging into.
>> Are you using the "root" user credential?  If so, some other issue may be
>> the cause - feel free to let us know if you have further questions.
>>
>> Specifically, the privilege CREATE_DATABASE is required to create a new
>> database in MySQL.  If you have been granted a non-root user account to log
>> into mysql hosted elsewhere (on a different server or VM), then the
>> administrator who gave you the account can create a blank database for you
>> (e.g. called "loris"), which the install script can then automatically
>> populate for you based on the default schema.
>>
>> Best,
>> Christine
>>
>>
>> On Thu, Nov 5, 2015 at 3:13 PM, Angela Lee <asl1 at ualberta.ca> wrote:
>>
>>> Hi,
>>>
>>> I'm currently trying to install LORIS on a virtual machine to see our
>>> lab would like to use it for an upcoming project. I'm having difficulty
>>> with running the installation script. I keep getting the message "Could not
>>> create the database with the root user provided".
>>>
>>> Thanks,
>>> --
>>> Angela Lee, Hon. BA&Sc, Student Research Assistant
>>> Department of Medicine - Neurology
>>> University of Alberta
>>>
>>> *Email:* asl1 at ualberta.ca
>>> *Phone: *1-(780)-248-1943
>>>
>>> _______________________________________________
>>> Loris-dev mailing list
>>> Loris-dev at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>
>>>
>>
>>
>> --
>>
>> christine.rogers at mcgill.ca
>> LORIS data systems | loris.ca
>> McGill Centre for Integrative Neuroscience| MCIN.ca
>> McConnell Brain Imaging Centre
>> Montreal Neurological Institute
>> McGill University | Montreal | Canada
>>
>
>
>
> --
> Angela Lee, Hon. BA&Sc, Student Research Assistant
> Department of Medicine - Neurology
> University of Alberta
>
> *Email:* asl1 at ualberta.ca
> *Phone: *1-(780)-248-1943
>



-- 

christine.rogers at mcgill.ca
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada
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From christine.rogers at mcgill.ca  Tue Nov 10 17:32:51 2015
From: christine.rogers at mcgill.ca (Christine Rogers)
Date: Tue, 10 Nov 2015 17:32:51 -0500
Subject: [Loris-dev] A question re MRI tables
In-Reply-To: <CAEpfQgLSghpPznFpfyw5isQQP9VgBpjcR_j9PaqhP0Wn5sirtw@mail.gmail.com>
References: <CAEpfQgLSghpPznFpfyw5isQQP9VgBpjcR_j9PaqhP0Wn5sirtw@mail.gmail.com>
Message-ID: <CALbt7NCJzYQpMWCV6f20aEQnYYJbEz-4rch-WUbm=mjE3j_EBw@mail.gmail.com>

Hi Naj,
Thanks for your question - that's feasible and we could put such a script
on the roadmap for improving the Imaging pipeline.
Loris is designed so that the protocol checks are defined based on an
official study-wide protocol (created at the beginning of a study), in
order to catch outlier data in incoming MRI scans, as opposed to being
defined based on a sample scanning session's data.  It is also common to
define protocol check using a range of allowable values for a given
parameter (e.g. TE_range: 3.0-4.0), which typically involves expert
adjustment of these acceptable parameter value limits.

Value range checks for MRI parameters for  t1, t2, dti and fMRI (e.g. TE,
TR values) can be edited directly in the front-end in the "MRI Protocol
Violations" submodule of the MRI Violated Scans module (under the Imaging
main menu), since these acquisition types are populated automatically in
the mri_protocol table.
This submodule can be viewed by accessing (e.g.)
https://demo.loris.ca/main.php?test_name=mri_violations&submenu=mri_protocol_violations

It may be helpful to consult the MySQL commands which load the mri_protocol
table with these default records for t1, t2, dti and fMRI.  These are
located in the default schema at:
https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L606

Best,
Christine


On Tue, Nov 10, 2015 at 9:49 AM, Najmeh Khalili-Mahani, Dr <
najmeh.khalilimahani at mcgill.ca> wrote:

> Hi,
>
> If I understand correctly, before starting to load the MRI data via Image
> Uploader, one must manually populate tables with information about the
> acquisition times of different sequences (T1, T2, TR, etc.)
>
> This is perhaps a naive question, but I wonder, might it be feasible for
> LORIS to have a PERL script that extracts those information from the DICOM
> or MINC headers and stores them without human intervention?
>
> Much thanks
> Naj
>
> ==================================
> Najmeh Khalili-Mahani, PhD
> Research Associate
> McGill Centre for Integrative Neuroscience
> Montreal Neurological Institute
> McGill University
>
> NW-143, 3801 University St.
> Montreal, QC, H3A 2B4
> Office: 514-398-1799
> email: najma at bic.mni.mcgill.ca
>
> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
>


-- 

christine.rogers at mcgill.ca
LORIS data systems | loris.ca
McGill Centre for Integrative Neuroscience| MCIN.ca
McConnell Brain Imaging Centre
Montreal Neurological Institute
McGill University | Montreal | Canada
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From david.macfarlane2 at mcgill.ca  Wed Nov 11 10:03:20 2015
From: david.macfarlane2 at mcgill.ca (Dave MacFarlane)
Date: Wed, 11 Nov 2015 10:03:20 -0500
Subject: [Loris-dev] A question re MRI tables
In-Reply-To: <CAEpfQgLSghpPznFpfyw5isQQP9VgBpjcR_j9PaqhP0Wn5sirtw@mail.gmail.com>
References: <CAEpfQgLSghpPznFpfyw5isQQP9VgBpjcR_j9PaqhP0Wn5sirtw@mail.gmail.com>
Message-ID: <BAY182-W36F68C581B187EFCF947C5F8130@phx.gbl>

Hi Najmeh,
That might be possible to do for some projects, but there's a few small problems in a general case for LORIS:
1. The mri_protocol table that you're referring to is meant to enforce the acceptable protocol range for a study, not describe the existing data. This is a form of QC to ensure that scans which are far out of range don't get inserted.2. The mri_protocol table is used to identify the scan type for scans as they come in based on the header ranges. There would need to be a better way to identify what type of scan and link it to the scan_types table (you can already use the series description instead of the ranges in the mri_protocol table, but there's no standard for series descriptions so you still need to manually link the series description to the protocol type in LORIS) and3. New projects don't have scans to extract the header information from, because the scans haven't been acquired yet.
Having a script to automatically populate the mri_protocol table based on an existing DICOM data set would certainly be a useful for some projects, though, for people who aren't concerned about point 1.
- Dave
From: najmeh.khalilimahani at mcgill.ca
Date: Tue, 10 Nov 2015 09:49:50 -0500
To: loris-dev at bic.mni.mcgill.ca
Subject: [Loris-dev] A question re MRI tables

Hi,
If I understand correctly, before starting to load the MRI data via Image Uploader, one must manually populate tables with information about the acquisition times of different sequences (T1, T2, TR, etc.)
This is perhaps a naive question, but I wonder, might it be feasible for LORIS to have a PERL script that extracts those information from the DICOM or MINC headers and stores them without human intervention? Much thanksNaj
==================================Najmeh Khalili-Mahani, PhDResearch AssociateMcGill Centre for Integrative NeuroscienceMontreal Neurological InstituteMcGill University
NW-143, 3801 University St.Montreal, QC, H3A 2B4Office: 514-398-1799email: najma at bic.mni.mcgill.ca

_______________________________________________
Loris-dev mailing list
Loris-dev at bic.mni.mcgill.ca
http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev 		 	   		  
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From najmeh.khalilimahani at mcgill.ca  Wed Nov 11 14:44:31 2015
From: najmeh.khalilimahani at mcgill.ca (Najmeh Khalili-Mahani, Dr)
Date: Wed, 11 Nov 2015 14:44:31 -0500
Subject: [Loris-dev] A question re MRI tables
In-Reply-To: <14097b7f48f54ee48db1720db0d95ed7@EXHUB2010-3.campus.MCGILL.CA>
References: <CAEpfQgLSghpPznFpfyw5isQQP9VgBpjcR_j9PaqhP0Wn5sirtw@mail.gmail.com>
	<14097b7f48f54ee48db1720db0d95ed7@EXHUB2010-3.campus.MCGILL.CA>
Message-ID: <CAEpfQgK_6O2x4dC2+3QCaDX-jn-pgtxzN6JUYV+yW1BMHp9qaw@mail.gmail.com>

Hi David, thank you this makes the logic very clear.

For my application (1) is unimportant, but (2) is important. However, I
would need some flexibility, as the MRI data is likely to be generated with
new experimental sequences.

I understand that DICOM inconsistencies could be an issue. But assume we
are getting data only from ONE scanner, and we make sure that the
DICOM-2-MINC is reliable for any image that is produced on THAT scanner.
Then I would assume that at the moment I am uploading a dicom file into my
MRI table of a new project, then it can simultaneously/automatically read
the header and fill in the values for MRI attributes. In this case we need
a table that accommodates all sequence attributes (FOV, resolution, TR,
TE1, TI, etc.), but allows to fill in only those that are pertinent to one
particular sequence.). Would this make sense and be feasible?

I am curious how this issue will be handled for a BIC-LORIS instance, where
one would expect the data to be collected over many experiments, with
customized sequence designs (e.g. work from Rick or Bruce's lab).

Much thanks
Naj




On Wed, Nov 11, 2015 at 10:03 AM, David MacFarlane, Mr. <
david.macfarlane2 at mcgill.ca> wrote:

> Hi Najmeh,
>
> That might be possible to do for some projects, but there's a few small
> problems in a general case for LORIS:
>
> 1. The mri_protocol table that you're referring to is meant to enforce the
> acceptable protocol range for a study, not describe the existing data. This
> is a form of QC to ensure that scans which are far out of range don't get
> inserted.
> 2. The mri_protocol table is used to identify the scan type for scans as
> they come in based on the header ranges. There would need to be a better
> way to identify what type of scan and link it to the scan_types table (you
> can already use the series description instead of the ranges in the
> mri_protocol table, but there's no standard for series descriptions so you
> still need to manually link the series description to the protocol type in
> LORIS) and
> 3. New projects don't have scans to extract the header information from,
> because the scans haven't been acquired yet.
>
> Having a script to automatically populate the mri_protocol table based on
> an existing DICOM data set would certainly be a useful for some projects,
> though, for people who aren't concerned about point 1.
>
> - Dave
> ------------------------------
> From: najmeh.khalilimahani at mcgill.ca
> Date: Tue, 10 Nov 2015 09:49:50 -0500
> To: loris-dev at bic.mni.mcgill.ca
> Subject: [Loris-dev] A question re MRI tables
>
>
> Hi,
>
> If I understand correctly, before starting to load the MRI data via Image
> Uploader, one must manually populate tables with information about the
> acquisition times of different sequences (T1, T2, TR, etc.)
>
> This is perhaps a naive question, but I wonder, might it be feasible for
> LORIS to have a PERL script that extracts those information from the DICOM
> or MINC headers and stores them without human intervention?
>
> Much thanks
> Naj
>
> ==================================
> Najmeh Khalili-Mahani, PhD
> Research Associate
> McGill Centre for Integrative Neuroscience
> Montreal Neurological Institute
> McGill University
>
> NW-143, 3801 University St.
> Montreal, QC, H3A 2B4
> Office: 514-398-1799
> email: najma at bic.mni.mcgill.ca
>
> _______________________________________________ Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>



-- 
==================================
Najmeh Khalili-Mahani, PhD
Research Associate
McGill Centre for Integrative Neuroscience
Montreal Neurological Institute
McGill University

NW-143, 3801 University St.
Montreal, QC, H3A 2B4
Office: 514-398-1799
email: najma at bic.mni.mcgill.ca
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