I would do the subtraction first then do the STC. On 04/01/2013 12:15 PM, Meryem Ayse Yucel wrote: > 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 > ===================== > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > intended only for the use of the individual or entity named above. If the > reader of the e-mail is not the intended recipient or the employee or agent > responsible for delivering it to the intended recipient, you are hereby > notified that you are in possession of confidential and privileged > information. Any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at (773) > 406-2464 or email. > > > 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 >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
