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

Help for FSL Archives


FSL Archives

FSL Archives


FSL@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

FSL Home

FSL Home

FSL  August 2009

FSL August 2009

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Setting up FEAT

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 10 Aug 2009 10:49:39 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (159 lines)

Hi,

One small thing to add as well - you should not use 12 DOF for the
main structural image (this controls the registration of the functional
to the structural image) since it is within-subject and so 6 DOF is
more correct.

All the best,
	Mark


On 10 Aug 2009, at 10:34, Mark Woolrich wrote:

> Eric,
>
> If you have not done so already, you will really benefit from going  
> through the Feat practicals (http://www.fmrib.ox.ac.uk/fslcourse)
>
> You want to establish if your data is alright, if the pre-processing  
> went alright, and if your EVs/model is set up alright.
>
> The EV you are using is a boxcar with period of 32 secs is quite  
> crude - you may need to consider more subtle modelling using 3  
> column format EVs (see the Feat prac)
> Also you can look at Melodic results to see if there is any  
> plausible activation, what timings that activation might have, and  
> if there are any nasty artefacts in the data.
>
> The best way to qualitatively assess the straightforward voxelwise  
> GLM stats is to go into the stats directory inside the feat  
> directory, and take a look at the zstat files in Fslview.
>
> To look for negative activations you need an extra contrast that is  
> [-1] ; presumably the one you have at the moment is just [1].
>
> Cheers, Mark.
> ----
> Dr Mark Woolrich
> EPSRC Advanced Research Fellow University Research Lecturer
>
> Oxford University Centre for Functional MRI of the Brain (FMRIB),
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK.
>
> Tel: (+44)1865-222782 Homepage: http://www.fmrib.ox.ac.uk/~woolrich
>
>
>
>
> On 10 Aug 2009, at 03:12, Eric Zalusky wrote:
>
>> I am new to FSL and functional analysis and would like to see if  
>> Iím setting
>> up my analysis correctly in FEAT.  Briefly the experiment uses two  
>> different
>> paradigms - each of which are scanned during two separate  
>> sequences.  The
>> first sequence alternates between thinking and passive activities.   
>> The
>> passive activity last 16 seconds and requires the subject to view 2  
>> rows of
>> asterisks for 3 seconds, followed by a 7 second pause.  Then the  
>> word yes or
>> no appears and the subject clicks the correct hand clicker.  Next  
>> there is a
>> 6 second pause then a thinking activity occurs. The subject is then  
>> given a
>> row of letters to memorize for 3 seconds.  This is followed by a 7  
>> second
>> pause and then a single letter appears and the subject must click  
>> yes/no if
>> the letter was in the previous row of letters.  Then there is a 6  
>> second
>> pause before a new set appears.
>>
>> The second paradigm uses the same timing but a different task -  
>> this is a
>> separate scan.
>>
>> When I use FEAT this is how I set up the analysis.
>>
>> DATA:
>> select analyze data
>> TR =2
>> High pass = 100
>> Volume = filled in automatically
>>
>> Prestats:
>> slice timing correction = interleaved
>> nothing else changed
>>
>> Stats:
>> Full Model Set Up:
>> Number of original EVs = 1
>> Basic Shape = square
>> Skip = 0
>> Off = 16
>> On = 16
>> Phase = 0
>> Stop after = -1
>> Convolution = Gamma
>> Phase = 0
>> Stddev = 3
>> Mean lag = 6
>> Yes to temporal derivative
>> Yes to Apply temporal filtering
>> Contrasts = 1
>> F-tests = 0
>>
>> Post-stats
>> I change nothing.  I use cluster thresholding, z=2.3 p=0.05
>>
>> Registration
>> I do not use the initial structural image
>> For the main structural image I use a high res T1 after BET at 12  
>> DOF.
>> The standard space is the default  MNI152 T1 2mm 12 DOF.
>>
>> Then I hit go and after the analysis is done, I go under Utils in  
>> FEAT and
>> upsample+overlay using the FEAT directory that was created and I  
>> upsample to
>> standard with the background image as the main structural.
>>
>> I do this the same for both paradigms that we scanned.
>>
>> When I go into FSL Viewer I am getting some weird activation.  I  
>> tried to
>> attach some pictures of what Iím seeing, but the files were too  
>> big, even
>> when I zipped them.  So I'll try to describe what I see in the viewer
>>
>> After I open my background image and add the activation, the
>> contrast/brightness is already set and there is significant  
>> activation
>> outside of the brain.  I can manually adjust this, but I can never  
>> seem to
>> get the image the same as my rendered thresh image.
>>
>> My questions are:
>> Am I setting up the analysis correctly in FEAT?
>>
>> Under the model set up, would I create more EVs, contrasts, or F- 
>> test?
>>
>> How do I correctly change the contrast and brightness to give me  
>> images that
>> are the same to the rendered thresh images?
>>
>> Is there a way to see negative activation?  I am able to see this  
>> on the
>> Siemens scanner.  I would like to be able to measure both the  
>> positive and
>> negative activation.
>>
>> Thanks,
>> Eric Zalusky
>>
>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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


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

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