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

[Neika Sharifian]

Hello! I thought I would send you an update which will hopefully help out
others they deal with the same issue. So the file format does affect the
script from running properly. What I had to do was restructure my marker
file to the test file format and then the script ran and created the .nirs
file.

Thank you for all of your help and fingers crossed, I won't have to bug you
with any more issues. :)

Neika Sharifian


On Mon, Feb 3, 2014 at 8:31 AM, Kreplin, Ute <U.Kreplin at 2011.ljmu.ac.uk>wrote:

> Hi there
>
> I used parallel port for the markers, so mine might look different to
> yours because of that. The markers in my file are the time (first collumn),
> the type of marker (20 30 40 are marker BIOPAC sets automatically, 1 and 4
> are the ones I set) and I can't remember what the third column is. The
> script uses only the first collumn so that bit shouldn't matter
>
> Try this. Open the 'gettriggers' file and change the 6 in line 18 to 0.
> Save and run the 'test_all' script. See what happens.
>
> BTW I don't think my triggers are sensitive to numbers, i.e. it will only
> give you one type of trigger (not 1, 2, 3 as shown in your file). You would
> have to moddify the 'gettriggers' script to make it sensitive to the type
> of triggers.
>
> 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: 03 February 2014 15:49
> To: homer-users at nmr.mgh.harvard.edu
> Subject: Re: [Homer-users] fNIRS, BIOPAC to Homer2 file conversion
>
> 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
> <mailto: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<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 Neika Sharifian [
> nsharif at ncsu.edu<mailto:nsharif at ncsu.edu>]
> Sent: 28 January 2014 16:41
> To: homer-users at nmr.mgh.harvard.edu<mailto: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><mailto: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><mailto:
> 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
> ><mailto: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><mailto:
> jared.dempsey at ttu.edu<mailto:jared.dempsey at ttu.edu>>
> Office: (806) 742-2891 x 267
> <tel:%28806%29%20742-2891%20x%20267><tel:%28806%29%20742-2891%20x%20267>
> Cell: (405) 269-3440<tel:%28405%29%20269-3440><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>> [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<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
> ><mailto: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><
> http://physiologicalcomputing.net> page on your website. I will let you
> know should I upload the files to nitrc.org<http://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><mailto:
> U.Kreplin at 2011.ljmu.ac.uk<mailto:U.Kreplin at 2011.ljmu.ac.uk>>
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>
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