From thoimis at gmail.com  Fri Feb 10 15:57:00 2017
From: thoimis at gmail.com (Thomas Johnson)
Date: Fri, 10 Feb 2017 13:57:00 -0700
Subject: [Nirfast] NIRFAST Slicer Not Starting
Message-ID: <A88B17D0-14FD-41BB-A167-B6A6293D5831@gmail.com>

Hello,

I have downloaded the most recent version of NIRFAST slicer (1.0.1) and cannot start it. I am thrown an exception on startup. The program cannot find the Qt framework, but it doesn?t say to install this framework on your website, so I am assuming this is some sort of bug. I am on macOS Sierra with Xcode installed. This is the error:

"Library not loaded: /usr/local/opt/qt/lib/QtSvg.framework/Versions/4/QtSvg?

Any ideas?

Thanks,

Thomas Johnson
Ph.D. Candidate
University of Calgary
thoimis at gmail.com <mailto:thoimis at gmail.com>
johnst at ucalgary.ca <mailto:johnst at ucalgary.ca>
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From jared.vicory at kitware.com  Mon Feb 13 09:31:48 2017
From: jared.vicory at kitware.com (Jared Vicory)
Date: Mon, 13 Feb 2017 09:31:48 -0500
Subject: [Nirfast] NIRFAST Slicer Not Starting
In-Reply-To: <A88B17D0-14FD-41BB-A167-B6A6293D5831@gmail.com>
References: <A88B17D0-14FD-41BB-A167-B6A6293D5831@gmail.com>
Message-ID: <CAOJ7+fZh4cT06-=BgLrzgKSK2vpxUy3KsceSAnxPJSrT4VhmVw@mail.gmail.com>

Hi Thomas,

Sorry for the inconvenience, it looks like the Qt Frameworks didn't get
pulled into the package properly.  I've uploaded a new version, please try
downloading it again and let me know if you have any further problems.


Thanks,
Jared

On Fri, Feb 10, 2017 at 3:57 PM, Thomas Johnson <thoimis at gmail.com> wrote:

> Hello,
>
> I have downloaded the most recent version of NIRFAST slicer (1.0.1) and
> cannot start it. I am thrown an exception on startup. The program cannot
> find the Qt framework, but it doesn?t say to install this framework on your
> website, so I am assuming this is some sort of bug. I am on macOS Sierra
> with Xcode installed. This is the error:
>
> "Library not loaded: /usr/local/opt/qt/lib/QtSvg.
> framework/Versions/4/QtSvg?
>
> Any ideas?
>
> Thanks,
>
> Thomas Johnson
> Ph.D. Candidate
> University of Calgary
> thoimis at gmail.com
> johnst at ucalgary.ca
>
> _______________________________________________
> Nirfast mailing list
> Nirfast at public.kitware.com
> http://public.kitware.com/mailman/listinfo/nirfast
>
>
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From thoimis at gmail.com  Mon Feb 13 12:32:33 2017
From: thoimis at gmail.com (Thomas Johnson)
Date: Mon, 13 Feb 2017 10:32:33 -0700
Subject: [Nirfast] Positive Jacobian Values
Message-ID: <E43BF702-746C-49D4-BB6A-0208A7811C8C@gmail.com>

Hello,

I am performing single wavelength forward simulations (800nm) on a custom 6-layer head mesh that models skin, skull, meninges, CSF, WM and GM. At a new different fibre separation lengths I end up with a Jacobian that has mostly positive values, while most other separation lengths give negative values. To me, this indicates the tissue is generating light! Can anyone help me out on this one? Here are things I am thinking:

- I have given each tissue type a separate index of refraction. Could this be reflection coming off the tissue boundary?

- There is a large region of CSF in my model. Is this an artefact of the diffusion approximation being unable to accurately simulate low scattering media?

Thank you,

Thomas Johnson

From h.dehghani at cs.bham.ac.uk  Mon Feb 13 13:35:14 2017
From: h.dehghani at cs.bham.ac.uk (Hamid Dehghani)
Date: Mon, 13 Feb 2017 18:35:14 +0000
Subject: [Nirfast] Positive Jacobian Values
In-Reply-To: <E43BF702-746C-49D4-BB6A-0208A7811C8C@gmail.com>
References: <E43BF702-746C-49D4-BB6A-0208A7811C8C@gmail.com>
Message-ID: <319a9516-1687-4e6b-c64b-c3edb8acc24b@cs.bham.ac.uk>

Hi
Are you looking at J.complete or J.complex?
If J.complete, remember that the values are rate of change of log 
intensity per a small change in mua.
So a positive value, just means a larger attenuation.
Hamid

On 13/02/2017 17:32, Thomas Johnson wrote:
> Hello,
>
> I am performing single wavelength forward simulations (800nm) on a custom 6-layer head mesh that models skin, skull, meninges, CSF, WM and GM. At a new different fibre separation lengths I end up with a Jacobian that has mostly positive values, while most other separation lengths give negative values. To me, this indicates the tissue is generating light! Can anyone help me out on this one? Here are things I am thinking:
>
> - I have given each tissue type a separate index of refraction. Could this be reflection coming off the tissue boundary?
>
> - There is a large region of CSF in my model. Is this an artefact of the diffusion approximation being unable to accurately simulate low scattering media?
>
> Thank you,
>
> Thomas Johnson
> _______________________________________________
> Nirfast mailing list
> Nirfast at public.kitware.com
> http://public.kitware.com/mailman/listinfo/nirfast
>

-- 
--------------------------
Hamid Dehghani, PhD, MIPEM
School of Computer Science
Acting Director, Physical Sciences for Health Doctoral Training Centre
University of Birmingham
B15 2TT
0121 414 8728
https://www.cs.bham.ac.uk/~dehghanh/mi-lab.html