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

Lyde, Elizabeth elizabeth.lyde at mavs.uta.edu
Tue Feb 13 11:05:04 EST 2018
Search archives: 
Hi Jonathan,


Thank you for your response. I have been able to figure out some of the problems I initially sent  in.


  1.  The color change of the channels from yellow (default) to green (channels of interest) indicates what channels we are looking at for the HbO overlay. For example when we input [0 0], we are indicating we want to look at all the channels at once hence all green, as oppose to inputting [10 3] which will only look at S10-D3 which would change the color of that channel to green.
  2.  You are correct, the pial ratio button had reverted to 0 by accident and adjusting the ratio brought the atlas brain back.


Thank you for your offer to look at the atlas. There are heavily concentrated dots that appear on the atlas. Initially I thought they corresponded to the sources and detectors but I no longer believe this to be true. They may correspond to activation hotspots; however, I cannot be 100% sure.


Elizabeth



________________________________
From: homer-users-bounces at nmr.mgh.harvard.edu <homer-users-bounces at nmr.mgh.harvard.edu> on behalf of Jonathan Perry <walwynperry at gmail.com>
Sent: Sunday, February 11, 2018 7:59:02 PM
To: moi moi
Subject: Re: [Homer-users] HbO/HbR concentration changes overlay on the Atlas using Digitizing points

Hello,

I am a bit late to the party, but I would like to supply input.


1. For digitizing points, this should not be a problem, but you would have to parse these into your .nirs file during your conversion script. This would just require x,y,z coordinates from your digitized point file to be input into the SD.SrcPos and SD.DetPos
- make sure these are in 'mm'
- Also, you seem to have figured out how to just use the digpts.txt file directly... so the above may be ignored

2. I don't believe the color change from yellow to green is of any concern,  I wonder if this was just a decision to avoid hot color overlays?
- This occurs in my upload as well and I seem to obtain reasonable results
- Any extra insight on this would be appreciated

3. For the disappeared brain..
- You can likely check the 'pial' radio button on the far left to bring back the brain
- I am curious if you have only run the 'run' level in Homer2 before inputting the .nirs file into AtlasViewer?  If not, make sure to run through the group option.
- This happened in my data as well if I had not named my file 'digpts.nirs' or had not run the file through the grouplevel in Homer2

4. As for the Monte Carlo, I don't believe the HbConc Overlay uses this.  The Monte Carlo is from my understanding reserved solely for the Sensitivity.  The HbConc is taken from the Homer2 output directly and should not require the Monte Carlo simulation.


Finally, I would be happy to take a look, but I cannot promise a quick turn-around.




Jonathan Perry

Master's Student

Department of Engineering Technology

University of Houston

 4734 Calhoun Rd., Room# 123

Houston, TX 77204-4021

Tel: (<tel:%28713%29%20743-4159>512)925-4910

On Thu, Feb 8, 2018 at 11:00 AM, <homer-users-request at nmr.mgh.harvard.edu<mailto:homer-users-request at nmr.mgh.harvard.edu>> wrote:
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Today's Topics:

   1. Re: HbO/HbR concentration changes overlay on the Atlas using
      Digitizing points (Sergio Novi)


----------------------------------------------------------------------

Message: 1
Date: Thu, 08 Feb 2018 11:47:27 +0000
From: Sergio Novi <novisl at ifi.unicamp.br<mailto:novisl at ifi.unicamp.br>>
Subject: Re: [Homer-users] HbO/HbR concentration changes overlay on
        the Atlas using Digitizing points
To: homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>
Message-ID:
        <CAKfhEdAFRCr0ffxz7By7MgTLsqmjc4T+Wc3tUJHzmiVXEDQ=wg at mail.gmail.com<mailto:wg at mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"

Hi Elizabeth,

these point seem unexpected to me. Could you send the Monte Carlo sensitive
profile (pictures) of channels near to these points?
As far as I know, the AtlasViwer should be using the MC simulations to
project the Hb concentrations to the brain.

Best,
S?rgio Novi

On Wed, Feb 7, 2018 at 9:48 PM Lyde, Elizabeth <elizabeth.lyde at mavs.uta.edu<mailto:elizabeth.lyde at mavs.uta.edu>>
wrote:

> 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<mailto:homer-users-bounces at nmr.mgh.harvard.edu> <
> homer-users-bounces at nmr.mgh.harvard.edu<mailto:homer-users-bounces at nmr.mgh.harvard.edu>> on behalf of Jahani, Sahar <
> SJAHANI at MGH.HARVARD.EDU<mailto: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<tel:%28713%29%20743-4159>
>
> 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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