[Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points

[Lyde, Elizabeth]

Hello all,


I had one last question regarding the HbO overlay function in Atlas.  I have notice that on my HbO overlay dots will appear on the Atlas. I'm unsure if these correspond to the activation or if it is an error.  Attached is an example of a finger tapping exercise where I would expect to see activation on the left motor cortex, where several of these dots appear.  Is anyone else experiencing this as well?


Many thanks,

Elizabeth



________________________________
From: homer-users-bounces at nmr.mgh.harvard.edu <homer-users-bounces at nmr.mgh.harvard.edu> on behalf of Jahani, Sahar <SJAHANI at MGH.HARVARD.EDU>
Sent: Saturday, January 20, 2018 7:20:25 PM
To: moi moi
Subject: Re: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points


Hello Elizabeth,



Follow these steps (you need digpts and groupResults.mat in the same folder):

  1.  go to Tools --> Register Atlas to digpts,
  2.  register Probe to Surface,
  3.  go to Tools --> Hb Conc Overlay,
  4.  insert your desired tmin and tmax range.





p.s: I am using Homer version v2.3 (https://www.nitrc.org/projects/homer2/)



Hope this will help.



Best,

Sahar





e: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points



Hello Elizabeth,



Jonathan Perry with my lab has been successful in overlaying Hb concentrations onto the standard brain. Since he is also busy working for NIRx, he might not be able to respond immediately, but I am confident he can provide some guidance soon.



Best,

Luca



Luca Pollonini, Ph.D.

Assistant Professor

Department of Engineering Technology

University of Houston

4734 Calhoun Rd., Room# 123

Houston, TX 77204-4021

Tel: (713) 743-4159

E-mail: lpollonini at uh.edu<mailto:lpollonini at uh.edu>

Web: polloninilab.com<http://polloninilab.com/>



From: <homer-users-bounces at nmr.mgh.harvard.edu<mailto:homer-users-bounces at nmr.mgh.harvard.edu>> on behalf of "Lyde, Elizabeth" <elizabeth.lyde at mavs.uta.edu<mailto:elizabeth.lyde at mavs.uta.edu>>
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: Thursday, January 18, 2018 at 6:15 AM
To: moi moi <homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>>
Subject: Re: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points



Hello again,



It turns out that the digpts.txt file can be used instead of the probe.SD file when trying to obtain Hb concentration plots via AtlasViewer as long as the groupResults file is also present.



I am now facing an issue where after clicking tools>>Hb Conc Overlay and adding the time range [tRangeMin tRangeMax], my meansList channels change from yellow to green. I'm unsure if this indicates an error has occur, or that it has processed the block average.



In addition, the brain disappears and I am unable to get HbO overlay. The Colormap Thresh range is [NaN NaN]. I can manually change the Colormap Thresh; however, nothing still appears.  (The HRF had a range between -1.5 and 1.5 microMolar in HomER.)



Does anyone have advice as to why this may be happening?

Many thanks,

Elizabeth







From: Lyde, Elizabeth
Sent: Tuesday, January 16, 2018 9:14:47 AM
To: moi moi
Subject: HbO/HbR concentration changes overlay on the Atlas using Digitizing points



Hello all,



I was curious if anyone has had success obtaining the HbO /HbR concentration overlay on Atlas using digitizing points rather than probe.SD files.



Or more simply, is there a way to convert the digitizing points into the probe.SD file?



Any advice or suggestions would be greatly appreciated.

Elizabeth
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