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

[Meryem Ayse Yucel]

Hi Ute,

I assume you have your own measurements, hence d (raw data) and t. If you
need to add SD structure to your .nirs file, what I would do is to use
SDgui to create the SD structure. Once you addpath to HOMER, you can type
SDgui on command window. It is easy to create your own SD file. Than it
will automatically have all fields that you need. Also you can get 'ml'
from SD.MeasList. Aux is not the same as t. If you have any auxiliary
measurements they appear in aux. s is your stimulus vector with ones at
the onset of each stimulus. You need to create it if you don't have one.

Meryem


> 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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