Yes. This would still be a problem. The calibration scan can either be used to get a single number or can be used to get voxel-wise values. For simplicity, lets say this is a constant across all voxels. The only thing that is a variable in the CBF equation would be the subtracted image values and delay time (time of slice acquisition . The values of the tag-control difference will be different at the top and bottom of the brain even if the flow is the same. Thus, you can't simply apply the slice-time correction algorithms for fMRI to ASL data.
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 Mon, Apr 1, 2013 at 12:15 PM, Meryem Ayse Yucel < mayucel@nmr.mgh.harvard.edu> 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.donald@gmail.com Subject: Re: [Freesurfer] slice timing To: Douglas N Greve greve@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: <CAKwrF_XJfg= PRTm2htZ12FN74VtP2qGzqffAGKeZBJO+pXDrQQ@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 greve@nmr.mgh.harvard.eduwrote:
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
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