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

[Sergio Novi]

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,
Sérgio Novi

On Wed, Feb 7, 2018 at 9:48 PM Lyde, Elizabeth <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 <
> 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 à Register Atlas to digpts,
>    2. register Probe to Surface,
>    3. go to Tools à 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
>
> Web: polloninilab.com
>
>
>
> *From: *<homer-users-bounces at nmr.mgh.harvard.edu> on behalf of "Lyde,
> Elizabeth" <elizabeth.lyde at mavs.uta.edu>
> *Reply-To: *"homer-users at nmr.mgh.harvard.edu" <
> 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>
> *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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