[Homer-users] fNIRS, BIOPAC to Homer2 file conversion

Mon Feb 3 10:49:24 EST 2014

Hello! Thank you for the advice!
I have been copying and pasting the filename, but I have stumbled upon
another error message. One thing I noticed about the file examples given
and my files is that the .mrk files are laid out different for my data.
When examining data for one participants, I put all files associated in the
current folder on Matlab (.nir.oxy, .nir, .mrk) and I came up with a
different error which may have to do with formatting of the mark files.

I have attached a copy of my marker file. In the example, I was hoping you
could shed some light on what each column and number represents. I assume
the first column is time, and I thought the second was the markers but it
starts with 20, 30, 40, so I wasn't completely sure.

I really appreciate your correspondence with me with all of these technical
difficulties. I'm relatively new to Matlab and trying to filter the fNIR
data has been a challenge thus far.

Best,
Neika Sharifian

On Mon, Feb 3, 2014 at 1:50 AM, Kreplin, Ute <U.Kreplin at 2011.ljmu.ac.uk>wrote:

> Hi Neika
>
> it looks like the script has trouble finding/identifying what file you
> want to use. Make sure that all files are in the same folder and/or are
> included in the matlab pathway. Make also sure that the file name is
> correct. Did you copy and paste the name or type it out? BIOPAC has a
> tendency to have weird spaces in their filenames that are difficult to see,
> try copy and pasting the file name and see if it makes a difference.
>
> Cheerio
>
> 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 Neika Sharifian [
> nsharif at ncsu.edu]
> Sent: 28 January 2014 16:41
> To: homer-users at nmr.mgh.harvard.edu
> Subject: Re: [Homer-users] fNIRS, BIOPAC to Homer2 file conversion
>
> Hello!
> I had a question about running the script. I keep getting this error
> message when I try and run my own data file in the matlab script and was
> wondering if you could help me figure out what's going wrong.
>
> Here is the error message:
> Error using fgets
> Invalid file identifier.  Use fopen to
> generate a valid file identifier.
>
> Error in fgetl (line 34)
> [tline,lt] = fgets(fid);
>
> Error in create_d (line 8)
>     temp = fgetl(fid); %reads in one line
>     of the file at a time
>
> Error in test_all (line 9)
> [t d aux] = create_d (file);
>
>
>
> I have also attached a screenshot of the script and the matlab program and
> a copy of one of my data files. Any advice would be appreciated!
>
> Thank you,
> Neika Sharifian
>
>
>
> On Fri, Jan 24, 2014 at 8:45 AM, Kreplin, Ute <U.Kreplin at 2011.ljmu.ac.uk
> <mailto:U.Kreplin at 2011.ljmu.ac.uk>> wrote:
> Hi Jared
>
> thanks for emailing me. The script doesn't work because I forgot to
> include test4 into the zip folder (oops).
>
> I'm just working on including it in the zip file so please check back if
> you get a version without it, this should be sorted soon.
>
> I atteched test4 to this email for you if you don't want to wait ;-)
>
> 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: Dempsey, Jared [jared.dempsey at ttu.edu<mailto:jared.dempsey at ttu.edu>]
> Sent: 24 January 2014 16:22
> To: Kreplin, Ute
> Subject: RE: fNIRS, BIOPAC to Homer2 file conversion
>
> Ute:
> Thank you so much for taking the time to create this.  It will help us all
> quite a bit.  I have a quick question.  When I follow your directions I
> come up the following error:
> Error using load
> Unable to read file 'test4': no such file or directory.
>
> Error in test_all (line 5)
> load test4
>
> Should this have been changed in the script?
>
> Best,
>
> Jared P. Dempsey, Ph.D.
> Addictive Disorders and Recovery Studies Program
> Department of Community, Family, and Addiction Services
> Texas Tech University
> Email: jared.dempsey at ttu.edu<mailto:jared.dempsey at ttu.edu>
> Office: (806) 742-2891 x 267<tel:%28806%29%20742-2891%20x%20267>
> Cell: (405) 269-3440<tel:%28405%29%20269-3440>
> Skype: jareddempsey
>
>
> -----Original Message-----
> From: homer-users-bounces at nmr.mgh.harvard.edu<mailto:
> homer-users-bounces at nmr.mgh.harvard.edu> [mailto:
> homer-users-bounces at nmr.mgh.harvard.edu<mailto:
> homer-users-bounces at nmr.mgh.harvard.edu>] On Behalf Of Kreplin, Ute
> Sent: Friday, January 24, 2014 9:20 AM
> To: homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu
> >
> Subject: [Homer-users] fNIRS, BIOPAC to Homer2 file conversion
>
> Hello all
>
>
>
> here is the link to the page where you can download a zip folder with a
> bunch of matlab scripts that convert the BIOPAC fNIRS file to Homer2 files.
> You will need matlab to run it. It might also not be perfect so feel free
> to improve it. I created the scripts about a year ago and have not worked
> with them since, I can therefore not really give much advice about what to
> do if it doesn't work. I hope though that it will help all of you who have
> been looking for something like this
>
>
>
> http://www.physiologicalcomputing.net/?page_id=2621
>
>
>
> Good luck with all your work
>
>
>
> Ute
>
>
>
> p.s. Re David Boas, please feel free to include a link to the scripts on
> the physiologicalcomputing.net<http://physiologicalcomputing.net> page on
> your website. I will let you know should I upload the files to nitrc.org<
> http://nitrc.org> in the future
>
>
>
> 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>
> ________________________________
>
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