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Subject:

Re: Slice Timing

From:

"MCLAREN, Donald" <[log in to unmask]>

Reply-To:

MCLAREN, Donald

Date:

Thu, 9 Aug 2012 16:52:03 -0400

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (73 lines) , Workbook8.pdf (73 lines)

In my present research, we are setting the microtime resolution to the
number of slices and the microtime onset to the temporal order of the
reference slice.

The microtime resolution doesn't seem to make a large difference,
whereas the microtime onset makes a larger difference. Attached is
some data at TR=1 and TR=2 for a variety of microtime resolution and
onsets.


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 Wed, Aug 8, 2012 at 11:47 PM, mmkleung <[log in to unmask]> wrote:
> Dear Drs. McLaren and Yamada,
>
> Sorry to interrupt but I notice that in SPM there's a description about the microtime resolution which has a default value of 16:
>
> "Do not change this parameter unless you have a long TR and wish to shift regressors so that they are aligned to a particular slice."
>
> However, in your discussions, it seems the value of microtime resolution is actually equal to the total number of slice and therefore, the default value of microtime resolution should be changed accordingly then. Am I correct?
>
> Thanks for your clarification!
>
> Cheers,
> Meikei
>
> ________________________________________
> From: SPM (Statistical Parametric Mapping) [[log in to unmask]] On Behalf Of MCLAREN, Donald [[log in to unmask]]
> Sent: Thursday, August 09, 2012 11:28 AM
> To: [log in to unmask]
> Subject: Re: [SPM] Slice Timing
>
> On Wed, Aug 8, 2012 at 10:48 PM, Kazuhiro Yamada <[log in to unmask]> wrote:
>> Dear Dr. MACLAREN
>>
>> Thank you very much for your helpful advice.  In thanking I would like to post this again.  I should be very grateful if you would kindly respond.
>> To make it somewhat more clear I reproduce here the essential part of my original message (please refer to "slice timing" in the archives of July 2012).  My original message was: An information on MAGNETOM family from Siemens tells that interleaved slice order starts at slice "1" when odd number of slices are taken, while it starts at "2" for even number of slices taken.  Therefore, for example, I set "slice order" at [2:2:24 1:2:23] for 24 slices and "reference slice" at 12.
>
>>>> I don't think you misunderstood slice-timing correction as you tried to pick the middle slice in terms of the acquired data, which is the 12th slice acquired out of 24 total slices. However, SPM wants to know the anatomical position of the reference slice, not the temporal position of the reference slice. I actually had to go back and check the spm code to make sure this is correct. Since your sequence was [2:2:24 1:2:23], then you want to use slice 24 as the reference because it is the 12th slice of data collected. Hope that clarifies the issue.
>
>> For this Gabor Oederland very kindly sent a message to me in August.  As Gabor, as well as yourself, says most appropriate "reference slice" should be 24 instead of 12 as I originally set.  (In this I probably misunderstood at some point of the concept of slice-timing correction).
>> Then "microtime resolution" should be set at 24 and "microtime onset" at 12.
>
>>>> These are correct.
>> With many thanks and best regards,
>>
>> Kazuhiro Yamada
>> Physiology, Univ. of Oita Faculty of Medicine.
>>
>>
>>

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