JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for SPM Archives


SPM Archives

SPM Archives


SPM@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

SPM Home

SPM Home

SPM  May 2010

SPM May 2010

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Slice Time Correction

From:

Feng Lu <[log in to unmask]>

Reply-To:

Feng Lu <[log in to unmask]>

Date:

Fri, 21 May 2010 09:42:10 +0800

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (111 lines)

Hi Thilo,
	
	Thank you for this mail because I met the same problem just now. But I feel confused. You said ' if you have an even number, the even slices are measured first and then the odd slices '. According to this, I think if the slice order specification from top to bottom and nslice = 28, the sequence should be [nslice:-2:2 nslice-1:-2:1]. Is it a small mistake?

-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Thilo Kellermann
Sent: 2010年5月19日 18:30
To: [log in to unmask]
Subject: Re: [SPM] Slice Time Correction

Hi Ed,

to make things a little more complicated: Usually you are right, that odd 
slices are measured first followed by the even ones. On a Siemens Trio 
machine, however, this is not always true (unless you use a self-programmed 
sequence). On a Trio the order depends on the number of slices - if you have 
an even number, the even slices are measured first and then the odd slices. 
Only if you have an odd number of slices the "normal" sequence (odd first, 
then even) is used.

In this case the slice order specification from top to bottom should be:
nslices = 28;
[nlsices-1:-2:1 nslices:-2:1]

The slices are numbered from bottom to top and the sequence gives the 
acquisition order. So if you are measuring from top to bottom and your number 
of slices is 28 on a Siemens Trio, the first slice you measure is no. 27, 
according to this numbering.

In this case slices 1 and 28 are measured in the middle within a TR and the 
choice of either one should be ok. If you are more interested in dorsal parts 
of the brain 28 might be more appropriate. Unfortunately when acquiring 
slices interleaved you never know, when the most interesting slice is being 
measured. If the region you are interested in is spreaded over more than one 
slice, this region will be measured at quite different times within a TR 
anyway (namely with a delay of about TR/2).

Good luck,
Thilo


On Monday 17 May 2010 19:53, Modestino, Edward J *HS wrote:
> Hello,
> I am in the process of attempting slice timing correction after completing
> realignment.  I have two questions: (1) I noticed that in the SPM8 manual
> there is mention that slice timing correction will be removed in the
> future.  Why?
>
> (2) My EPI data is collect on a Siemens 3T MAGNETOM Trio in an interleaved
> (odd slices first: odd 1:27 followed by even 2:28) sequence staring from
> the top to bottom with 28 slices and a TR of 2 seconds.  Slice timing is
> not working.  So, here are my specs.  Please let me know if I have
> something wrong:
>
> number of slices: 28
> TR: 2
> TA: 2-2/28
> Slice Order:  I am choosing the option for interleaved top->bottom, so I
> follow the input examples given there: TOP TO BOTTOM accoring to John
> Christopher
> interleaved top->down [nslices:-2:1, nslices-1:-2:1]
> 28:-2:1, 28-1:-2:1
> displays [28 26 24 22 20 18 16 14 12 10 8 6 4 2 27 25 23 21 19 17 15 13 11
> 9 7 5 3 1]
>
> Shouldn't this order be the following instead [1 3 5 7 9 11 13 15 17 19 21
> 23 25 27 2 4 6 8 10 12 14 16 18 20 22 24 26 28]
>
> What does it mean that bottom slice = 1, as we are going top to bottom and
> the top slice is 1?  How can the bottom slice be 1?
>
> Reference slice: 2 (or I could use slice 27)
>
> Thanks,
> Ed Modestino
>
> Edward Justin Modestino, Ph.D.
> Postdoctoral Research Associate
> Ray Westphal Neuroimaging Laboratory
> Division of Perceptual Studies
> Department of Psychiatry and Neurobehavioral Sciences
> University of Virginia

-- 
Thilo Kellermann
RWTH Aachen University
Department of Psychiatry and Psychotherapy
JARA Translational Brain Medicine
Pauwelsstr. 30
52074 Aachen
Germany
Tel.: +49 (0)241 / 8089977
Fax.: +49 (0)241 / 8082401
E-Mail: [log in to unmask]

__________ Information from ESET NOD32 Antivirus, version of virus signature database 5127 (20100519) __________

The message was checked by ESET NOD32 Antivirus.

http://www.eset.com


 

__________ Information from ESET NOD32 Antivirus, version of virus signature database 5133 (20100520) __________

The message was checked by ESET NOD32 Antivirus.

http://www.eset.com
 

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001
2000
1999
1998


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager