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

Wed Mar 6 11:28:48 EST 2013

This is correct, my script is designed to take the MES file (in csv format) and convert it to nirs format.

The "sampling period" i.e. sampling rate on our machine is fixed to 0.1s and I don't think we can easily change it.  I would have thought that 0.5s was acceptable given that fMRI provides sampling rates of 1 to 2 seconds but I guess it depends what you're looking at.  Sorry I can't be more help there.

Cheers,

Rebecca

-----Original Message-----
From: Marco Montalto [mailto:montaltomarco at onvol.net] 
Sent: 06 March 2013 15:10
To: homer-users at nmr.mgh.harvard.edu
Cc: Rebecca Dewey
Subject: Re: [Homer-users] Format of .nirs file and Sample Data

Dear Rebecca,

I collected data using a Hitachi ETG-4000. I analysed the data on the device itself in Integral Mode. Now I am aware that Homer2 does not allow one to import concentration files - one must have files with the raw data. So the .csv files I exported from the ETG-4000 are rather useless in this case. But I have noticed that for each subject, together with the .csv files (tagged HBA) containing concentrations for oxy, deoxy and total Hb,  I have a .csv file with the tag MES, which I just got to know stands for measurement data. So it seems that when using Integral Mode, the exported data includes a .csv file containing the raw intensity data. My question is therefore the following: from your experience using the ETG-4000 can I use the matlab script you so kindly prepared to convert these MES .csv files into .nirs files for use with Homer2?

Also, one more question: when I was collecting the data I was not very knowledgable about NIRS and I therefore assumed that a sampling period of 0.5 seconds would suffice? Do you think that this sampling rate is way too low?

Thanks and looking forward to your replies.

Regards,
Marco

On 06 Mar 2013, at 15:18, Rebecca Dewey <Rebecca.Dewey at nottingham.ac.uk> wrote:

> Hi Ute,
> 
> Which NIRS system are you using?  If it is Hitachi, I have written a script to convert the output csv file (the raw probe one, not the chromophore ones) into a .nirs for Homer.  It is available on http://nitrc.org/projects/hitachi2nirs/.  Even if you are not using Hitachi, the later part of the script may be of some use to you in terms of figuring out the variable structure.  Let me know if you have any questions regarding the script if you choose to use it.
> 
> Cheers,
> 
> Rebecca
> 
> Rebecca Dewey PhD
> Research Fellow in Neuroimaging
> National Institute for Health Research Nottingham Hearing Biomedical 
> Research Unit Ropewalk House, 113 The Ropewalk, Nottingham, NG1 5DU
> 
> t: +44 (0)115 82 32638 (direct) | t: +44 (0)115 82 32600 (reception) | 
> w: www.hearing.nihr.ac.uk
> 
> 
> 
> 
> -----Original Message-----
> From: homer-users-bounces at nmr.mgh.harvard.edu 
> [mailto:homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of Kreplin, 
> Ute
> Sent: 06 March 2013 12:59
> To: homer-users at nmr.mgh.harvard.edu
> Subject: Re: [Homer-users] Format of .nirs file and Sample Data
> 
> 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 nm
> r.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://g
> h.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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