A QUICK GUIDE TO USE CARTOOL. from electrode location importing through segmentation

[Iman]

Hi,

I have provided a quick illustrated guide for CARTOOL. 

Hope it helps and save your time.

Any comment or thought is welcome!

Best,

Iman

====================

Iman M.Rezazadeh, PhD

Center for Mind and Brain

University of California, Davis

ireza...@ucdavis.edu

[Yoder, Paul J]

I agree with most of the decisions in the manual, except for the KL peak that indicates the optimal number of maps. Instead of using the 1^st peak, the tutorials explicitly recommend against using the 1^st, use the subsequent KL peak at which there is a local minimum CV.

--
This is a message sent from the Cartool Community group cartoolcommunity.unige.ch
 
To unsubscribe from this group, send an email to cartool+u...@googlegroups.com
 
Please note: unsuscribing from the group also unsuscribes you from the Cartool registration and download of Cartool.. if you just want to set how you receive messages, go to: groups.google.com/group/cartool/subscribe

[Michel]

Hi Iman

Can you tell us how you got the maps that you display on the first page of your tutorial. Don't you think that they look strange? Are you sure that the order of electrodes in he xyz and the eph file correspond?

Best

Christoph

_______________________________

Prof. Christoph M. Michel, PhD

Functional Brain Mapping Laboratory
Dept. of Fundamental Neurosciences
University Medical School
1, rue Michel-Servet
1211 Geneva, Switzerland
Tel. +41-22-379-54-57
email:christop...@unige.ch
Web-page: http://brainmapping.unige.ch/

--
This is a message sent from the Cartool Community group cartoolcommunity.unige.ch
 
To unsubscribe from this group, send an email to cartool+u...@googlegroups.com
 
Please note: unsuscribing from the group also unsuscribes you from the Cartool registration and download of Cartool.. if you just want to set how you receive messages, go to: groups.google.com/group/cartool/subscribe

<An Illustarated Guide for Cartool-31052012.pdf>

[Murray Micah]

Hi Iman,

Great that you are using Cartool. I see you work with Clifford Saron. Please send him my regards, as we go way back.

 

At any rate, I am not sure if you have already done so, but you might want to interact with Lee Miller as he was here on sabbatical and has a fairly solid understanding of the analyses and file formats of Cartool. He might therefore be able to provide some “local” help.

 

Like Paul Yoder, I would also encourage you to take a look at some of the tutorials covering the analyses in Cartool (e.g. Murray et al. 2008 Brain Topography as well as Brunet et al 2011 Computational Intelligence and Neuroscience). It is a fairly “tricky” issue to select the optimal number of clusters, though we do make some recommendations.

 

Like Christoph, I think your maps look a bit off. If you open your electrode coordinate file are the electrodes where they should be relative to their neighbours?

 

More generally, there is an online reference guide with Cartool that includes many screen captures and explains many of the processing steps as well as all of the file types handled by and/or created by Cartool. This might save you some time/efforts.

 

Best and good luck with your research,

Micah

 

De : car...@googlegroups.com [mailto:car...@googlegroups.com] De la part de Iman
Envoyé : jeudi, 31. mai 2012 22:10
À : car...@googlegroups.com
Objet : [Cartool Community] A QUICK GUIDE TO USE CARTOOL. from electrode location importing through segmentation

--

[Iman]

Thanks Paul for your comments. I am agree on it! 

On Thursday, May 31, 2012 1:18:38 PM UTC-7, Paul wrote:

I agree with most of the decisions in the manual, except for the KL peak that indicates the optimal number of maps. Instead of using the 1^st peak, the tutorials explicitly recommend against using the 1^st, use the subsequent KL peak at which there is a local minimum CV.

 

From: car...@googlegroups.com [mailto:cartool@googlegroups.com] On Behalf Of Iman
Sent: Thursday, May 31, 2012 3:10 PM
To: car...@googlegroups.com
Subject: [Cartool Community] A QUICK GUIDE TO USE CARTOOL. from electrode location importing through segmentation

 

Hi,

I have provided a quick illustrated guide for CARTOOL. 

Hope it helps and save your time.

Any comment or thought is welcome!

Best,

Iman

====================

Iman M.Rezazadeh, PhD

Center for Mind and Brain

University of California, Davis

ireza...@ucdavis.edu

 

--
This is a message sent from the Cartool Community group cartoolcommunity.unige.ch
 

To unsubscribe from this group, send an email to cartool+unsubscribe@googlegroups.com

[Iman]

Dear Christoph,

Thanks for your comments.

Here I have attached my xyz file which made from EEGLAB. It would be great if you check it out and let me know your comments. BTW, what do you think about top maps on the page 8 of my tutorials? Does it sound?

Cheers,

Iman

On Thursday, May 31, 2012 1:43:55 PM UTC-7, Michel wrote:

Hi Iman

Can you tell us how you got the maps that you display on the first page of your tutorial. Don't you think that they look strange? Are you sure that the order of electrodes in he xyz and the eph file correspond?

Best

Christoph

_______________________________

Prof. Christoph M. Michel, PhD

Functional Brain Mapping Laboratory
Dept. of Fundamental Neurosciences
University Medical School
1, rue Michel-Servet
1211 Geneva, Switzerland
Tel. +41-22-379-54-57

email:christoph.michel@unige.ch
Web-page: http://brainmapping.unige.ch/

On May 31, 2012, at 10:09 PM, Iman wrote:

Hi,

I have provided a quick illustrated guide for CARTOOL. 

Hope it helps and save your time.

Any comment or thought is welcome!

Best,

Iman

====================

Iman M.Rezazadeh, PhD

Center for Mind and Brain

University of California, Davis

ireza...@ucdavis.edu

--
This is a message sent from the Cartool Community group cartoolcommunity.unige.ch
 

To unsubscribe from this group, send an email to cartool+unsubscribe@googlegroups.com

[Markus Plank]

Hi Iman,

Please allow me to chime in. Did you use the code I wrote which can be downloaded from the Cartool pages?

Best,

Markus

--

Markus Plank, Ph.D.

Postdoctoral Researcher

Institute for Neural Computation

UC San Diego

e-mail: mpl...@ucsd.edu

phone: +1 (858) 717 - 3183

To unsubscribe from this group, send an email to cartool+u...@googlegroups.com

 
Please note: unsuscribing from the group also unsuscribes you from the Cartool registration and download of Cartool.. if you just want to set how you receive messages, go to: groups.google.com/group/cartool/subscribe

<TTTTASDMSI_003_forSOBI_4.xyz>

[Iman]

Hi Micah:

Great to hear from you!  I will definitively convey your greetings to him, your old dude:)  

What a coincidence! Today, Cliff, Lee and I had a wonderful meeting and we all are trying to employ your great software our works. We sat together and talked about concepts of microstates which sound great for all of us.  We all are trying to  learn the software from its online help but there are some question points for us. That is why I drafted the tutorial and posted to be commented and refined by this community. As I stated the purpose of my tutorial is a very quick and illustrated guide through running which I have learnt through studying the online help and many posts in this forum, but it is not a substitute for the online help . 

I have uploaded the xyz file to see if there is sth wrong with the electrodes coordination ! 

It would be also great if there is a video that shows the users how to deal with Cartool and we are thoroughly open to help.

Cheers,

Iman 

On Thursday, May 31, 2012 2:30:54 PM UTC-7, Micah wrote:

Hi Iman,

Great that you are using Cartool. I see you work with Clifford Saron. Please send him my regards, as we go way back.

 

At any rate, I am not sure if you have already done so, but you might want to interact with Lee Miller as he was here on sabbatical and has a fairly solid understanding of the analyses and file formats of Cartool. He might therefore be able to provide some “local” help.

 

Like Paul Yoder, I would also encourage you to take a look at some of the tutorials covering the analyses in Cartool (e.g. Murray et al. 2008 Brain Topography as well as Brunet et al 2011 Computational Intelligence and Neuroscience). It is a fairly “tricky” issue to select the optimal number of clusters, though we do make some recommendations.

 

Like Christoph, I think your maps look a bit off. If you open your electrode coordinate file are the electrodes where they should be relative to their neighbours?

 

More generally, there is an online reference guide with Cartool that includes many screen captures and explains many of the processing steps as well as all of the file types handled by and/or created by Cartool. This might save you some time/efforts.

 

Best and good luck with your research,

Micah

 

De : car...@googlegroups.com [mailto:cartool@googlegroups.com] De la part de Iman

Envoyé : jeudi, 31. mai 2012 22:10
À : car...@googlegroups.com
Objet : [Cartool Community] A QUICK GUIDE TO USE CARTOOL. from electrode location importing through segmentation

 

Hi,

I have provided a quick illustrated guide for CARTOOL. 

Hope it helps and save your time.

Any comment or thought is welcome!

Best,

Iman

====================

Iman M.Rezazadeh, PhD

Center for Mind and Brain

University of California, Davis

ireza...@ucdavis.edu

 

--
This is a message sent from the Cartool Community group cartoolcommunity.unige.ch
 

To unsubscribe from this group, send an email to cartool+unsubscribe@googlegroups.com

[Iman]

Hi Markus,

I have not used any codes from here. What part do you mean I should use your code?

Best,

Iman

<TTTTASDMSI_003_forSOBI_4.xyz>

[Lee Miller]

Hi Iman (and Hi Micah, Hi Christoph!),

You can find Markus' handy code for EEGLAB at  http://sites.google.com/site/cartoolcommunity/files.  I also have a  ditty to write .els and .eph files from ERPLAB structures, which I'll  give to Denis to post.

I'm happy to help you figure this out.  It may be most efficient to take  this off-list for a few days, meet to look over your data in person, and come back to the Community when we have any additional questions or tips.  Just contact me today and we'll get started.

Best,
Lee

To unsubscribe from this group, send an email to cartool+u...@googlegroups.com

[Iman]

Thanks, Lee!  I am totally agree on your points !

Just sent you an email re available time to contact,

Cheers,

Iman