[Homer-users] SD geometry warning and baseline removal

[Perdue, Katherine]

Hi all,

I think you will have that SD geometry warning if you add new datasets to a directory when you have already processed some of them. The SD structure is different (because some subjects have procResult and others don’t), but it is not important for your analysis. Try just saying “Load” and if there is a real problem Homer2 will notify you or refuse to run.

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 Apr 13, 2016, at 3:16 AM, Jörn M. Horschig <jorn at artinis.com<mailto:jorn at artinis.com>> wrote:

Hi Gavin,

Concerning your first point, could you send me one of your datafiles (oxy-file)? Then I can have a look if the warning comes from our side (i.e. something happening during the conversion from the oxy-file to Homer) or not. In any case, I wouldn't worry too much as long as your distances are okay. I am not sure about the warning, but maybe it is indeed happening because you are using more than one distance? Just a wild guess though.

All the best,
Jörn

--
Jörn M. Horschig, PhD, Software Engineer
Artinis Medical Systems  |  +31 481 350 980
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.artinis.com&d=CwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=WA_1JFk0jL0vhJomc_fx9OiqPcSooSCVS1ccIEWVyPAom48e4TZPmckeX2WU3s83&m=N7rvT7M4530leEsnu5ImgA0mogfec1Qy-SXIwL3mLmo&s=gBjJ_l5Dq2JidIAkSqEEN0G5wfCLxnWI475nKrvjyyc&e=


-----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] On Behalf Of Tempest.GAVIN at unice.fr<mailto:Tempest.GAVIN at unice.fr>
Sent: Thursday, March 10, 2016 17:23
To: homer-users at nmr.mgh.harvard.edu<mailto:homer-users at nmr.mgh.harvard.edu>
Subject: [Homer-users] SD geometry warning and baseline removal

Dear HomER users,
I have found the forum a very helpful source of information and I have a couple of questions of my own about data analysis.
Briefly; I have data converted from Oxysoft (.oxy) to .nirs files. Data were collected during 60min cycling exercise from two 1x4 squares with a SD distance of either 3 or 4cm. I am using HomER to process the data (filter, remove and correct artefacts etc.) before export.
1. When I load the files into HomER, I receive the following error:
‘WARNING: More than One SD geometry found. Might cause errors’. What is the reason for this and how should it be fixed?
2. I am not using stimuli markers or block averaging sections of the
data; however the first two minutes of each dataset are ‘resting’
measures (baseline).  I would like to remove the baseline data from the subsequent signal or to use these data as a reference; perhaps incorporating these data would influence the motion correction functions
(?) Does HomER include a function to account for an initial baseline during the processing stages?
Any help is much appreciated,
Gavin

Research Fellow
Laboratory LAMHESS
University of Nice, France

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