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[SCIRUN-USERS] Re: RE: RE: Defibrillation tutorial.

Chronological Thread 
  • From: Jess Tate <>
  • To: "Kharche, Sanjay" <>
  • Cc: "" <>
  • Subject: [SCIRUN-USERS] Re: RE: RE: Defibrillation tutorial.
  • Date: Wed, 7 Aug 2013 15:47:14 -0600

Hi Sanjay,

There is are a couple of example in the Fwd/Inv toolkit to do what you would like.  The document is available on the website with the SCIRun tutorials, and there is a link to the example networks in the menu of the SCIRun interface.   Look at the potential based FEM and BEM forward problem examples.

You will need to convert your data into a format SCIRun can read, this includes the voltage data and some form of geometry (a list of points for the voltage values).  There are several types to choice from, so this hopefully won't be too difficult.  The easiest may be saving the data as a matlab matrix and a list of points in ascii format (.pts), but it will depend your data.  


On Aug 7, 2013, at 12:31 AM, Kharche, Sanjay wrote:

Dear Jess, All

I have installed SCIRun in Linux, and it works fine - thanks for the advice.

I have the next question now. I have a heart simulation where the output is stored as a voltage map (a binary dump of floats). This heart simulation is done using code I developed and is not in SCIRun format. I would like to put this voltage map into the torso (in place of your heart segmentation) to get a body surface potential map, and if possible ECGs at a few electrodes. Can you summarise the way to do this?


From: Jess Tate []
Sent: 06 August 2013 00:08
Cc: Kharche, Sanjay
Subject: Re: [SCIRUN-USERS] RE: Defibrillation tutorial.

Hi Sanjay,

There is a problem with tcl in which it  sometimes doesn't correctly keep the same filename, but the file is usually read in correctly.  In any case, you don't seem to be reading any data at all or else you would have an error in the convertfieldtotexture module.  Have you been successful in loading data previously?  You can try to load some other data from the SCIRunData set.  Look for .nrrd or .nhdr files (change the file type to nrrd in the readfield module).  There are some in the heart-ischemia and FEMesher directories.  If you cannot read or visualize any files, then there may be an issue with your particular setup.  


On Aug 4, 2013, at 9:10 AM, Kharche, Sanjay wrote:

Hi Jess

Thanks for the pointers. I have as yet not been able to carry out sec. 4.1 visualisation and the details are as follows.

I downloaded the data again, this time the tgz file rather than the zip file. I noticed that the torso_segmentation_si.fld file is the same file size in both the zip and tgz distributions. So perhaps the data are not corrupt. After constructing the network, checking the X,Y,Z in the textureslices module, I left the colormap unaltered, and the output is the image as attached. I can see the slice planes, and the slice widget, but no torso. I tried to go thru' the slices using the buttons in the textureslices, but could not see much.

About errors, there is a dos prompt like window that comes up when running SCIRun in windows. In this window, when I reach the view (using the view scene module) stage, I get an error:
I/O error: no such file or directory
In fact, when I select, set and execute the torso_segmentation_si.fld in the ReadFld module, I get this error. So I think somehow, the data is just not being read. Another error to mention may be that once the network is ready, and I get the view as in the attached png, I tried to confirm that the fld file is correct. When I open the ReadFld UI, I see that an electrode*.fld is in the file field, not torso_segmentation_si.fld.

Can you comment?


From: Jess Tate []
Sent: 04 August 2013 06:00
To: Kharche, Sanjay
Subject: Re: [SCIRUN-USERS] Defibrillation tutorial.

Hi Sanjay,

If you do not see anything in the view window, you should make sure that the x y and z planes have been checked in the showtextureslice UI.  If there are no errors then that is the most likely issue.  It helps to see leave the color map unaltered at first (do not make zero transparent).  If you see the slice widget (looks like a small sphere) but nothing else, you may have moved it off the volume.  create a new shotextureslices module (and select the planes).  If that doesn't work or you see slices that are gray or all blue, then the data could be corrupted.  Make sure you are loading the correct file (torso_segmentation_si.fld) from the SCIRunData file.  You may need to download the data again.  

This should work.  The only thing that you have to change in the modules is checking the planes as mentioned.  Don't change any other settings in the module (at first).  There is an off chance that there are some graphics card compatibility issues since the texture data is meant to use the shader functionality in the hardware, however I haven't seen major problems with this module, especially if you haven't had any other graphics issues with SCIRun.  


On Aug 3, 2013, at 9:49 AM, Kharche, Sanjay wrote:


I am using the windows 64 bit version 4.6 of SCIRun to work thru' the defibrillation tutorial.

With reference to the pdf tutorial, I am trying to implement "sec. 4.1 Loading the Data set". I have attempted the instructions several times, and my network looks like fig 4.1. However, when I try to view the result, I cannot see the torso. It seems the data is not being read in, although the Read module does have the fld file in it. Please can someone indicate what could be missing.

many thanks


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