[Homer-users] Format of .nirs file and Sample Data

Wed Mar 6 07:59:00 EST 2013

Hi David,

it doesn't, I'm sorry. I've seen these instructions, but don;t really know what to do with them. I also looked at the example file and still don't really know what to do.

The .NIRS file that I can make out of my matlab file has none of these fields.

Do I need to use the raw data or can I use oxy and deoxy data? Do I need to input all of these fields (at least ones) manually? And where do I get them from? I sort of see where t and d come from and some of SD, but not all. Will I need to phsycally measure the devise to get SrcPos? Is nSrcs the number of light sources the divice has? Is s my list of triggers? And is aux exactly the same as t, or how does it differ?

Thanks
Ute

Ute Kreplin
PhD Candidate
Liverpool John Moores University
Rm 312 Tom Reilly Building
Byrom Street
Liverpool, L3 3AF
U.Kreplin at 2011.ljmu.ac.uk
________________________________
From: homer-users-bounces at nmr.mgh.harvard.edu [homer-users-bounces at nmr.mgh.harvard.edu] on behalf of David Boas [dboas at nmr.mgh.harvard.edu]
Sent: 06 March 2013 12:21
To: homer-users at nmr.mgh.harvard.edu; David Boas
Subject: [Homer-users] Format of .nirs file and Sample Data

Dear Ute,

To create a proper .nirs file please look at the Homer2 Users Guide at
http://www.nmr.mgh.harvard.edu/DOT/resources/homer2/documentation.htm

It is the first page of the documentation after the Table of Contents that describes how to make the .nirs file. It is on page 4.

On that same web page, next line down, you can find a link to download sample data. Please download that zip file. In the directory Example1_Simple_Probe, you will find Simple_Probe.nirs that will provide an example of this .nirs file.

I hope that helps you.

David

On 3/6/13 5:12 AM, Kreplin, Ute wrote:

Hi David,

sorry I've jsut realised that I can open the raw file in matlab and turn them into matlab files (see attached), but it still won't let me save them into .NIRS it tells me that SD, t, etc are missing. How do I create them?

Thanks
Ute

Ute Kreplin
PhD Candidate
Liverpool John Moores University
Rm 312 Tom Reilly Building
Byrom Street
Liverpool, L3 3AF
U.Kreplin at 2011.ljmu.ac.uk<mailto:U.Kreplin at 2011.ljmu.ac.uk>
________________________________
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 David Boas [dboas at nmr.mgh.harvard.edu<mailto:dboas at nmr.mgh.harvard.edu>]
Sent: 04 March 2013 23:16
To: homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>
Subject: Re: [Homer-users] Questions about Homer2 developer version and AtlasViewerGui

It looks like you are trying to do a CVS update as jdubb rather than as an anonymous user. As jdubb, you would need his password.

I am not exactly sure how you set up your CVS.

Here are the instructions from the web site. Please set up your CVS again following these instructions and checkout a new version of HOMER2 to a new directory. Once you get the checkout right, it should give you all the files you need for AtlasViewer.

The developer's version of Homer2 can be obtained at orbit.nmr.mgh.harvard.edu using the Current Version System access. This is the source code repository that the developers are using to constantly update the code. By setting up the CVS download using one of the procedures indicated below, you will be able to easily update your current version of Homer2 at any time, rather than waiting for official releases.
In linux, the command line access is with
cvs -d :pserver:anonymous at orbit.nmr.mgh.harvard.edu:/cvsroot/homer checkout HOMER2

(Note that all of the above command, from "cvs" to "HOMER2," needs to appear on one line)

In Windows, there are several CVS clients available. One that we have used is TortoiseCVS. And we have also used SmartCVS.

On the Mac, also, there are several CVS clients available. One that we have used is SmartCVS.

Note that these are free CVS clients. They may indicate that you have to pay for the full version, but the less functional free versions are perfectly sufficient to maintain easy updates of Homer2.

On 3/4/13 5:59 PM, Silvia Bisconti wrote:
Dear all,

I have two questions:

1) I are trying to use the developer version of Homer2 through CVS and when we try to update it, the output shows the following error message:

In C:\HOMER2: "C:\Program Files (x86)\CVSNT\cvs.exe" -q update -P -d
CVSROOT=:ext:jdubb at orbit.nmr.m<mailto:CVSROOT=:ext:jdubb at orbit.nmr.m><mailto:ubb at orbit.nmr.m><mailto:ubb at orbit.nmr.m>gh.harvard.edu<http://gh.harvard.edu><http://gh.harvard.edu>:/cvsroot/homer

cvs [update aborted]: end of file from server (consult above messages if any)

Error, CVS operation failed

2) When I try to use AtlasViewerGui in Matlab, I am not able to see the brain because the files (Head file, Pial file and Ref points file) do not exist in the current directory.

How should I fix that?

Could anyone suggest me any solution?

Thank you,

Silvia Bisconti

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