[Homer-users] Formatting for NIRS-SPM

[Drew Halliday]

Hi Danushka,

Thanks for your reply.  As you probably know, Homer2 saves the
pre-processed data into a single .nirs file that contains the Hb data, and
event onsets and duration (as well as numerous other things).  I think
NIRS-SPM needs a Matlab file containing Hb (oxy, deoxy and maybe total as
well), sampling rate, number of channels, and wavelengths, and then a
separate file specifying event onsets and duration.  So an initial step for
bringing data from Homer2 to NIRS-SPM would be to extract this information
from the .nirs file and to restructure it in a way that NIRS-SPM accepts.
I understand that a new version of NIRS-SPM is due out in August, but I
don't know if there is anything in place to facilitate importing data from
Homer2.

I suppose there is enough variability between paradigms and systems to the
extent that the conversion process is difficult to generalize, but please
let me know if you have any thoughts.

Thanks again,
Drew

On Tue, Jul 14, 2015 at 6:37 PM, Danushka Bandara <danushkabandara at gmail.com
> wrote:

> I have experience with NIRS_SPM but not that familiar with HOMER, so if
> you can specify how your processed data looks like, I can possibly help you.
> Cheers,
>
> On Sun, Jul 12, 2015 at 10:13 PM, <gramigna at unicz.it> wrote:
>
>> Hi,
>> I'm also interested in a way to bring data pre-processed with Homer2 to
>> Nirs-Spm in order to perform group analysis and to visualize the results
>> on MRI brain.
>> Any suggestion would be greatly appreciated.
>> All the best
>>
>>
>> > Hi all,
>> >
>> > I am also interested in the answer to Drew's question. Who has
>> experience
>> > with bringing .nirs files to NIRS-SPM?
>> >
>> > Kind regards,
>> > Laurien Nagels-Coune
>> >
>> > Laurien Nagels-Coune | Visiting Graduate Researcher at UCLA | Research
>> > Master in Clinical and Cognitive Neuroscience, track Cognitive
>> > Neuroscience | I6073928 | Faculty of Psychology and Neuroscience |
>> > Maastricht University
>> > ________________________________________
>> > From: homer-users-bounces at nmr.mgh.harvard.edu
>> > [homer-users-bounces at nmr.mgh.harvard.edu] On Behalf Of Drew Halliday
>> > [d.halliday at ucl.ac.uk]
>> > Sent: 03 July 2015 18:35
>> > To: homer-users at nmr.mgh.harvard.edu
>> > Subject: [Homer-users] Formatting for NIRS-SPM
>> >
>> > Dear Homer2 Users,
>> >
>> > I am attempting to bring data that I've pre-processed in Homer2 to
>> > NIRS-SPM to run GLM analyses and am following what appears to be
>> > relatively out-dated protocol from NIRS-SPM (2009).  I'm wondering if
>> > anyone has had success with importing to NIRS-SPM and if so, if they
>> might
>> > be able to help.
>> >
>> > Specifically, following the conversion option and after specifying that
>> > the data are from "HomER Software" I select the .nirs file and am then
>> > asked to import a .mat file, which according to the available protocol,
>> > comes from exporting Hb concentrations through 'delta Concentrations' in
>> > the  'Data Display Controls' menu.  My suspicion is that this
>> description
>> > is based on an older version of HomER/EasyNIRS and that this option no
>> > longer exists in Homer2.  This .mat file is to contain the Hb
>> > concentrations, so is presumably what is exported through the export HRF
>> > option.  I tried loading a .nirs file and them writing a .mat file with
>> > procResult.dcAvg, but receive an error that the .mat file should be
>> > binary.  NIRS-SPM doesn't accept .txt or .csv.
>> >
>> > Any direction would be greatly appreciated.
>> >
>> > Cheers,
>> > Drew
>> >
>> > _______________________________________________
>> > 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.
>> >
>> >
>>
>>
>> _______________________________________________
>> Homer-users mailing list
>> Homer-users at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
>>
>
>
>
> --
>
> Danushka Bandara
> about.me/danushka.bandara
> [image: Danushka Bandara on about.me]
>   <http://about.me/danushka.bandara>
>
> _______________________________________________
> 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.
>
>


-- 
Drew Halliday
Research Assistant
Medical Physics & Bioengineering
University College London
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/homer-users/attachments/20150714/f2060cc4/attachment.html