WM and CSF are c[23].nii
You should read the manual chapter for segmentation.
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From: Umesh Venkatesan [[log in to unmask]]
Sent: Monday, February 24, 2014 12:34 AM
To: Watson, Christopher
Cc: [log in to unmask]
Subject: Re: [SPM] Extracting time series from noise ROIs
Thanks for your response. How do I obtain the TPMs for the the individual subjects? I didn't see this as part of the seg output, but maybe I'm misunderstanding.
Umi
On Sun, Feb 23, 2014 at 11:36 PM, Watson, Christopher <[log in to unmask]<mailto:[log in to unmask]>> wrote:
You don't need to "build ROIs" using Marsbar. You can just use the WM & CSF images as masks and get the mean from those. It may not be automated, per se, but you can throw a few commands in a script so that for each subject you just feed it that individual's TPM's, or add it to a batch file. Or whatever you prefer when you automate other stuff in SPM.
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From: SPM (Statistical Parametric Mapping) [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Umesh Venkatesan [[log in to unmask]<mailto:[log in to unmask]>]
Sent: Sunday, February 23, 2014 11:15 PM
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: [SPM] Extracting time series from noise ROIs
Dear SPMers,
Novice question here, but could someone please advise on the best way(s) to extract WM and CSF mean signals from individual functional data?
The only way I could think of doing this was to take masks created from the Segment (or New Segment) module and build ROIs using MarsBaR, from which the mean signals can be extracted. But I'm wondering if there is a more automated procedure, perhaps directly taking the segmentation output and extracting signal. Do any scripts for this exist?
Thanks,
Umi
--
Umesh "Umi" Venkatesan, M.S.
Graduate Student, Adult Clinical Psychology
Staff Therapist, Penn State Psychological Clinic
The Pennsylvania State University
419 Bruce V. Moore Building
University Park, PA 16802
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