[Homer-users] (no subject)

[Chiu, Bryan (PHTH)]

Hi,

my temp fix so far is to set " lstSS=[9,10,11,12]' " which overwrites what is done in line 61. This fixed the problem so far and gets me the results which I need.

by stepping, I have found the culprit is "lst = find(ml(:,4)==1);" .
 lst = [1,     3,     5,     7,     9,    11,    13,    15,    17,    19,    21,    23]' . When we reach line 61 it will then pull lstSS=[17,19,21,23]'. ml doesn't appear to be the shape that it 'wants', but as far as that goes I am having trouble understanding where this originates from.

Does this mean that SD.MeasList is problematic?

Regards,

- Bryan
________________________________________
From: homer-users-bounces at nmr.mgh.harvard.edu [homer-users-bounces at nmr.mgh.harvard.edu] on behalf of Chiu, Bryan (PHTH) [bryan.chiu at ubc.ca]
Sent: Tuesday, August 19, 2014 2:38 PM
To: homer-users at nmr.mgh.harvard.edu
Subject: Re: [Homer-users] (no subject)

Hi,

After setting the breakpoint I found that what the error originates from in line 71 is that it takes posM and lstSS and compares the two to take a smaller part of posM and use that further on. This is where the index issues originate, the lstSS is a list which is calling rows of the matrix that do not exist (posM is length 12, but lstSS is between 17 to 23.

Will continue debugging and let you know what the result is.

- Bryan
________________________________________
From: homer-users-bounces at nmr.mgh.harvard.edu [homer-users-bounces at nmr.mgh.harvard.edu] on behalf of Huppert, Ted [huppertt at upmc.edu]
Sent: Tuesday, August 19, 2014 12:21 PM
To: homer-users at nmr.mgh.harvard.edu
Subject: Re: [Homer-users] (no subject)

In matlab, you can always set a debug break point and stop the program on the line to investigate the issue.    Its really hard to diagnose problems without your exact dataset and the exact processing pipeline.

In matlab type:
"dbstop in hmrDeconvTB_SS3rd at 71”

This will set a debug break right at the line you are having troubles with.  You can then try to look at the variables and diagnose the problem.  Alternatively, you can use the command “dbstop if error”  which will stop anywhere in the program that an error occurred.

My guess from looking at that function is that your measurement list variable in the NIRS file is not sorted by wavelength (e.g. The two wavelength indexes in the 4th column are mixed).  E.g. The line "lst = find(ml(:,4)==1);” finds entries that are in the second 1/2 of the ml variable.

David-
The quick solution is to change lines 58,59 and 73 to read (e.g.) “rhoSD( lst(iML)) =  “ instead of "rhoSD(iML) = "



----------------
Theodore Huppert, PhD
Associate Professor
Departments of Radiology and Bioengineering
University of Pittsburgh
Email: huppertt at upmc.edu
Phone: (412) 647-8459



"Insanity: doing the same thing over and over and expecting different results"-  Einstein

From: <Chiu>, "Bryan (PHTH)" <bryan.chiu at ubc.ca<mailto:bryan.chiu at ubc.ca>>
Reply-To: "homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>" <homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>>
Date: Tuesday, August 19, 2014 at 2:04 PM
To: "homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>" <homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>>
Subject: Re: [Homer-users] (no subject)

hmrDeconvTB_SS3rd

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