Hi all,
Thank you so much for your response. That list will be very helpful -
thanks Mike!
Yes, we would like to try and see if physio correction makes a
difference, in particular locally to some structures in the brain stem.
We were going to look at it in a couple of participants to start with
and using the PNM toolbox. However, Matt, if you have any other idea for
a more general method of physiological noise clean-up, we'd love to hear
about it.
...very happy to give feedback on our progress and on what difference it
makes, if any, in terms of tSNR etc when we have gotten a bit further.
Best
Miriam
On 14/06/2016 20:16, Glasser, Matthew wrote:
My experience with the phyiso files is that in a basic PNM model, RVT
is the main trace that does anything and it pulls out some but not all
of the apparent global physiological noise in the data. I would say
the physiological traces are useful for understanding various aspects
of the data in the context of data cleanup and sources of artifacts,
but given that they are not available for all datasets and do an
imperfect job at removing the physiological noise we'll need another
method for general physiological noise cleanup of HCP data.
Peace,
Matt.
From: <[email protected]
<mailto:[email protected]>> on behalf of "Hodge,
Michael" <[email protected] <mailto:[email protected]>>
Date: Tuesday, June 14, 2016 at 2:07 PM
To: "Harms, Michael" <[email protected] <mailto:[email protected]>>,
Miriam Klein-Flügge <[email protected]
<mailto:[email protected]>>,
"[email protected] <mailto:[email protected]>"
<[email protected] <mailto:[email protected]>>
Subject: Re: [HCP-Users] Participants with good physiological data
Hi Miriam,
Mike Harms is correct that the files haven’t been QC’d. They have,
however, gone through a minimal automated process that checks that the
files are of reasonable length and that we have the trigger pulses
that should allow for the data to be reliably matched to the imaging
sequence. When those conditions aren’t met, the files aren’t
produced. That’s why there are a fairly high percentage of subjects
without physio data. To help you find subjects with data, I’ve
attached a list of physio files I pulled from the drive we use for
syncing with Amazon S3 and making Connectome-in-a-Box.
Regards,
Mike
*From:*[email protected]
<mailto:[email protected]>
[mailto:[email protected]] *On Behalf Of *Harms,
Michael
*Sent:* Tuesday, June 14, 2016 9:10 AM
*To:* Miriam Klein-Flügge <[email protected]
<mailto:[email protected]>>;
[email protected] <mailto:[email protected]>
*Subject:* Re: [HCP-Users] Participants with good physiological data
Hi,
We have not QC’ed the physiological traces. If you start working with
that data, we would appreciate it if you could give us feedback on
your experience.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: [email protected] <mailto:[email protected]>
*From: *<[email protected]
<mailto:[email protected]>> on behalf of Miriam
Klein-Flügge <[email protected]
<mailto:[email protected]>>
*Date: *Tuesday, June 14, 2016 at 8:52 AM
*To: *"[email protected]
<mailto:[email protected]>" <[email protected]
<mailto:[email protected]>>
*Subject: *[HCP-Users] Participants with good physiological data
Dear all,
I wondered whether there is any documentation about which participants
have good physiological monitoring data. I may have missed this
somewhere but all I managed to do is to download an entire subjects'
unprocessed rfMRI dataset to see if their folder contains the physio
regressors in the “LINKED_DATA” folder (then I know at least whether
they exist, not necessarily whether they are good). Is there a way to
avoid having to download and then delete the ones that don’t?
Thanks,
Miriam
--
Miriam Klein-Flügge
Sir Henry Wellcome Postdoctoral Fellow
Department of Experimental Psychology
University of Oxford
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you are not the intended recipient, be advised that any unauthorized
use, disclosure, copying or the taking of any action in reliance on
the contents of this information is strictly prohibited. If you have
received this email in error, please immediately notify the sender via
telephone or return mail.
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The materials in this message are private and may contain Protected
Healthcare Information or other information of a sensitive nature. If
you are not the intended recipient, be advised that any unauthorized
use, disclosure, copying or the taking of any action in reliance on
the contents of this information is strictly prohibited. If you have
received this email in error, please immediately notify the sender via
telephone or return mail.
--
Miriam Klein-Flügge
Sir Henry Wellcome Postdoctoral Fellow
Department of Experimental Psychology
University of Oxford
_______________________________________________
HCP-Users mailing list
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