[Homer-users] Changing laser name in Homer2

Wed Mar 4 23:03:05 EST 2015

Hi Shannon,

I think you are all set if the MeasList matches with the source 3/6 swap. I haven’t seen MeasListMask or MeasList_USBorder, hopefully someone else will weigh in if they have experience with those variables and think they will impact your analysis.

best,
Katherine

On Mar 3, 2015, at 3:00 PM, Shannon Michelle Burns <smb02011 at mymail.pomona.edu<mailto:smb02011 at mymail.pomona.edu>> wrote:

Hi Katherine,

Sorry, I was emailing from home before and had mixed up MeasList with MeasListMask. So yes the real MeasList file only differs on source 3 and source 6. The MeasListMask and MeasList_USBorder still differ on multiple rows, but they're all the same depending on which set of data this particular file is in (before laser break and after laser change), so I assume it's ok to adjust these values as well?

Btw thanks so much for your time answering all this!

Shannon

On Mar 3, 2015, at 9:41 AM, Perdue, Katherine <Katherine.Perdue at childrens.harvard.edu<mailto:Katherine.Perdue at childrens.harvard.edu>> wrote:

Hi Shannon,

The MeasList field in the SD structure is the key Homer2 uses to determine what channel goes with each column of data in the d matrix. So as you said, if you change the SD structure, the channel order might seem fine when you open it in Homer 2, but the data itself might no longer match up with the “key” provided in the SD file. That would mean that the channel locations are actually scrambled.

There might be more than one line different between the 2 MeasLists if you have source C/F in more than one channel. The important thing to check would be in that first column, where the source numbers are listed, that the difference is only that your source C (3) has been replaced by source F (6). All of the other rows should be in the same order between the 2 MeasLists. If that is not the case, it can be fixed, but it is a little more tricky!

I am not sure about MeasList_USBorder, I haven’t heard of that before. Does it match the MeasList for an individual file?

best,
Katherine

-------------
Katherine Perdue, PhD
Research Fellow in Pediatrics
Labs of Cognitive Neuroscience
Division of Developmental Medicine
Boston Children's Hospital
Office Phone: 857-218-5214

On Mar 3, 2015, at 11:56 AM, Shannon Michelle Burns <smb02011 at mymail.pomona.edu<mailto:smb02011 at mymail.pomona.edu>> wrote:

Hi Katherine,

Thanks for your reply. Are you saying that the channel order would seem the same when opening Homer, but in actuality it changed between the two groups and therefor the Homer display is incorrect? I edited a few of the SD files last night and there were more than one cell different in the MeasList and MeasList_USBorder.

Best,
Shannon

On Mar 3, 2015, at 7:52 AM, Perdue, Katherine <Katherine.Perdue at childrens.harvard.edu<mailto:Katherine.Perdue at childrens.harvard.edu>> wrote:

Hi Shannon,

It is probably good to double check the measurement lists in your old and new files and make sure that the only change between the two is the exchange of source C for source F. You can check this by looking at SD.MeasList in the old and new files, and making sure that the only difference is that in the first column, source C, represented by a 3, is replaced by source F, represented by 6.

If you just replace the SD file to be the same across all subjects, it will make the error go away, but it doesn’t change the fact that the channels may be in a different order in your two groups depending on how your measurement list was set up.

best,
Katherine

-------------
Katherine Perdue, PhD
Research Fellow in Pediatrics
Labs of Cognitive Neuroscience
Division of Developmental Medicine
Boston Children's Hospital
Office Phone: 857-218-5214

On Mar 3, 2015, at 12:25 AM, Shannon Michelle Burns <smb02011 at mymail.pomona.edu<mailto:smb02011 at mymail.pomona.edu>> wrote:

It worked, thank you very much!

________________________________
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 Hörmetjan Yiltiz <hyiltiz at gmail.com<mailto:hyiltiz at gmail.com>>
Sent: Saturday, February 28, 2015 10:17 PM
To: homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>
Subject: Re: [Homer-users] Changing laser name in Homer2

Simply load the .nirs file as .mat file (load a.nirs -mat) and then change the SD struct in it to make them universal across all .nirs files. This same scenario also occured to me.

祝好，
========================
He who is worthy to receive his days and nights is worthy to receive* all
else* from you (and me).
                                                 The Prophet, Gibran Kahlil

On Sun, Mar 1, 2015 at 3:27 AM, Shannon Michelle Burns <smb02011 at mymail.pomona.edu<mailto:smb02011 at mymail.pomona.edu>> wrote:
Hi all,

I've been running an fNIRS experiment using The TechEn system and analyzing with Homer2, but after about half of my subjects one of the lasers used in my array (C) stopped working on the machine, so I had to switch the SD file to a different laser (F). It's in the exact same position, but is just another letter. Because of this though my data set currently cannot be analyzed together as half of them have a different laser in the probe geometry. Can anyone advise me how to edit the .nirs files in the second half of my data so that I can change laser F to laser C and make Homer think it's the same geometry again?

Thanks so much!

Shannon Burns
Cultural Neuroscience Laboratory
Pomona College Neuroscience Dept.
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