Thanks Steve. Sorry if this is repetitive, I just want to get this
straight....
> First, we generally discourage concatenation of different session time
> series for first-level analyses.
So you are saying that multiple time series acquired during the SAME
scanning session get analyzed separately, than combined at higher-level FEAT
analysis?
I (mistakenly?) thought higher-level analysis was for across scanning
sessions and/or across subjects, but not within a single scanning session
that had multiple time series acquired.
----- Original Message -----
From: "Stephen Smith" <[log in to unmask]>
To: <[log in to unmask]>
Sent: Wednesday, April 09, 2003 3:51 AM
Subject: Re: [FSL] preparing functional data for FEAT
> Hi.
>
> First, we generally discourage concatenation of different session time
> series for first-level analyses, but recommend separate analyses which
> then get combined at higher-level FEAT anlayses, for various practical and
> theoretical reasons.
>
> To run avwmerge, assuming, for each session, that your 120 volumes have
> their numbers in the "00001" part, you want
> avwmerge -t mp_001 mp_001_00???.img
> you can check the order it will use just by typing
> echo mp_001_00???.img
>
> Doing the above will allow easy use of the "delete volumes" option in
> FEAT.
>
> Thanks, Steve.
>
>
>
> On Wed, 9 Apr 2003, Mark Pinsk wrote:
>
> > Hi, just started w/ FSL. I haven't found a clear answer on something
that
> > seems simple.
> >
> > Typical experiment session: Ten 4-minute EPI "runs" (TR=2, 120
measurements
> > per run, so total of 1200 measurements).
> >
> > Each measurement is an Analyze file (hdr+img) named like this:
> > subject_run#_measurement# (ex: mp_001_00001.img).
> >
> >
> > My first inclination is to avwmerge all 1200 files into one big Analyze
> > file. First question: will avwmerge know what order to put all that
data
> > in (given the numbering scheme shown above) ?
> >
> > Also, the "delete volumes" option in FEAT does not make sense then,
since
> > it will just delete the first few measurements of run 1, but not the
first
> > few measurements of subsequent runs since they are all merged into one
> > file. So then it looks like I need to first, manually delete the first
> > few .img/.hdr files of each and every run, THEN use avwmerge to put it
all
> > together, then set delete volumes to 0. Does that seem right to you?
> >
> > If that IS correct, then I will have to create a very long design matrix
> > (unless the conditions occur in same exact order for each run). Is that
> > correct?
> >
> > Alternatively, I imagine analyzing each run separately, then doing some
> > sort of group analysis, but that seems counterintuitive to me.
Especially
> > since all these runs were acquired in same experimental session.
> >
> > Any help clearing this up would be very much appreciated, thanks!
> > Mark
> >
>
> Stephen M. Smith MA DPhil CEng MIEE
> Associate Director, FMRIB and Analysis Research Coordinator
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
>
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>
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