[Homer-users] AtlasViewerGUI Hb Concentration Plot

Tue Aug 29 09:45:29 EDT 2017

Dear Sahar,
thank you for your prompt reply.
Unfortunately, I still have problems in using the function.
I’m using the Matlab Runtime. So I open AtlasViewer and then I select the folder with the preprocessed .nirs data. Then, if I directly import the SD structure from the .nirs file (measurement unit cm) I have the situation in FIG1. If I previously convert the SD structure in mm and I create a probe.SD file (that for what I understand it is the right thing to do) I have the situation in FIG2.
So, in the first case, ‘register probe to surface’ is enabled but the optodes disposition is wrong, while in the second case the disposition seems more reasonable (with the obvious problem of some offset) but ‘register probe to surface’ is disabled.
The only way in which I can register the probe to the surface is using some standard digitized points and ‘Register Atlas to dig points’ but then, as I explained previously, I am not able to plot the Hb concentration (nothing happens when I click on Hb Conc Overlay and/or I select something in drop down box).

Thank you very much for all you assistance.
Selene

________________________________
Da: homer-users-bounces at nmr.mgh.harvard.edu <homer-users-bounces at nmr.mgh.harvard.edu> per conto di Jahani, Sahar <SJAHANI at mgh.harvard.edu>
Inviato: lunedì 31 luglio 2017 23:15:30
A: homer-users at nmr.mgh.harvard.edu
Oggetto: Re: [Homer-users] AtlasViewerGUI Hb Concentration Plot

Dear Selena,

Here you can find the instruction for using the overlay function.

1)     Add Homer folders and subfolders to your Matlab path,
2)     Change your Matlab path to the folder where your groupResults.mat is available,
3)     Open AtlasViewerGUI,
4)     Go to tools menu and import your probe.SD file,
5)     Register probe to the surface,
6)     From the Tools menu, select Hb Conc Overlay,
7)     Select an appropriate time range: [tRangeMin tRangeMax]. (The time range which you want to see the averaged Hbo/HbR changes on the Atlas),
8)     From the drop down box in the Image Display section, you can select HbO Conc, HbR Conc and so on. Also, under the drop down box, you are able to specify the colormap range (specifying an appropriate colormap range will result in a complete probe HbO/ HbR overlay on the Atlas), channel numbers (default is displaying all channels), and Condition (put the number of your intended condition) and then press the Enter key.
Hope this will help you.
Please let me know if you have any comments or questions.

Thank you,
Sahar

From: homer-users-bounces at nmr.mgh.harvard.edu [mailto:homer-users-bounces at nmr.mgh.harvardedu] On Behalf Of Carrara Selene
Sent: Thursday, July 27, 2017 4:16 AM
To: homer-users at nmr.mgh.harvard.edu
Subject: [Homer-users] AtlasViewerGUI Hb Concentration Plot

Dear all,

I have seen on NITRC that the new release of Homer2 (v 2.2) gives the opportunity to overlay images of Hb concentrations on the cortex. Unfortunately, when I try to use this function it does not work properly. So, I would like to ask if you can explain which are the steps to use this function, in order to understand where is my mistake.

Actually, I simply click on HbO or HbR Conc in 'Image display' but I have no results (nothing happens on the screen, it plots only the colorbar), in addition I cannot modify 'condition'.

(I am using v 2.2 with MCR_R2016a 64 bit)

Thank you for your attention,

Selene Carrara

Selene Carrara, Eng.

fMRI-fNIRS Laboratory

IRCCS Fondazione Don Gnocchi

Via Capecelatro 66

20152 Milan, Italy

+39 02 40308074

[Banner Campagna SMS]<http://5x1000.dongnocchi.it/>
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