[Homer-users] AtlasViewerGUI Hb Concentration Plot

Tue Sep 5 10:12:21 EDT 2017

Dear Sahar,

In complement to your response Jonathan Perry wrote on 02/09/2017 the 
following:

/So in order to view the HbConc on AtlasViewer, you have a few things to 
work out.//
//
//Run homer processing opt through the group level//
//The groupResults is saved automatically and will be needed.//
//You will need the digpts.nirs file as well as the groupResults.//
//Also make sure you have the SDunits in your nirs file in "mm" not "cm"/

/
/

/
/

However, after having applied both instructions I have a warning message 
in the overlay function:

/Warning: Projection is Empty
/

/
/

The way I understand it is that the data used for the overlay function 
are in group.procResult.dcAvg of the groupResults.mat file.

I've check it and I have the correct data in it.

I feel like I'm missing some dummy step, so for the record I'll sum up them:

/
/

/
/

/
//1- I Ran homer processing opt through the group level//
//2- Saved the group result.mat//
//3- Copied the digpts.txt file as well as the groupResults.mat file in 
the subjects folder//
//4- I've check both cm and mm as SDunits with no results/

/5- Registered Atlas to Dig points/

/6- Registered Probe to Surface/

/7- Hb Conc Overlay/

/8- Choose the correct time window/

/
/

And here I've got my warning message.

Any Help would be very appreciated !

I use:

matlab 2015a with all toolboxes

Atlas viewer V2.2

Homer v2.2

/
/

Best,

Sébastien/
/

/
/

/
/

Le 31/07/2017 à 23:15, Jahani, Sahar a écrit :
>
> 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.harvard.edu] *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/>
>
>
>
> _______________________________________________
> Homer-users mailing list
> Homer-users at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and properly
> dispose of the e-mail.

-- 
Signature Email ISAE-SUPAERO

Sébastien SCANNELLA
Research scientist in Neuroergonomics

ISAE SUPAERO - Institut Supérieur de l'Aéronautique et de l'Espace
10 avenue Edouard Belin - BP 54032 - 31055 TOULOUSE CEDEX 4 FRANCE - 
http://www.isae-supaero.fr
Tel +33 5 61 33 87 59 - Fax (+33) 5 61 33 83 30
Plan d'accès/Access map <http://plan.univ-toulouse.fr/#783> - Page 
personnelle <http://quickscience.e-monsite.com/>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20170905/d7ea7726/attachment-0001.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ibhgdoghpgmddako.png
Type: image/png
Size: 15101 bytes
Desc: not available
Url : http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20170905/d7ea7726/attachment-0001.png 