Doug,
I use preproc-sess 's -stc up option to time correct my slices. I only
have 6 slices.
Donald,
I am not calculating absolute CBF values using the calibration scan. I
pre-process the data and then either surround-subtract or just subtract
tag from control to get CBF, would it still be a problem to use slice time
correction?
Thanks,
Meryem
Message: 11
Date: Fri, 29 Mar 2013 13:40:42 -0400
From: "MCLAREN, Donald" <mclaren.don...@gmail.com>
Subject: Re: [Freesurfer] slice timing
To: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAKwrF_XJfg=prtm2htz12fn74vtp2qgzqffagkezbjo+pxd...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
If you are using ASL, you do not want to use Slice timing. You must compute
the CBF maps and keep the slice timing intact.
Removing the time delay between slices will lead to the wrong CBF values as
the CBF equations have the time delay in the equation.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Fri, Mar 29, 2013 at 1:08 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu>wrote:
> what are you using to do STC? I think by default FSL will move it to the
> middle slice, but there is probably a way to make take into account the
> fact that the slices are not uniform over the TR. You should contact the
> list of the software you are using to get a definative answer.
> doug
>
>
> On 03/29/2013 11:37 AM, Meryem Ayse Yucel wrote:
> > Hi,
> >
> > I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am
> > wondering when I do slice time correction does that move all slices to
> the
> > mid of TR that is 1.5 s prior in time or, it moves them to the timing of
> > the mid slice, which would be the mid of image acquisition aorund 0.6 sec
> > prior in time with respect to the end of TR.
> >
> > Thank you,
> >
> > Meryem
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> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
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