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  2001

FSL 2001

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: FEAT

From:

Xavier Chitnis <[log in to unmask]>

Reply-To:

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

Date:

Tue, 18 Sep 2001 22:40:41 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (162 lines)

Dear Steve,

I combined the three sessions for each subject using FEAT group statistics - three input volumes per subject, registration & group stats (a single group for each subject)

Many thanks

Xavier


>Hi - I assume you've combined the data using group stats in FEAT - or did
>you use concatenation of the time series' in the end?
>
>Thanks
>
> Stephen M. Smith
> Head of Image Analysis, FMRIB
>
> Oxford University Centre for Functional MRI of the Brain
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726  (fax 222717)
>
> [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve
>
>On Tue, 18 Sep 2001, Xavier Chitnis wrote:
>
>> Dear Steve,
>>
>> I have processed our subjects for this experiment to the point of having
>> combined the three sessions for each subject. We have two groups of subjects
>> (n=6 in each); what would be the best way of proceeding to a group
>> comparison?
>>
>> Many thanks again for your help,
>>
>> Xavier
>>
>>
>> -----Original Message-----
>> From: Xavier Chitnis [mailto:[log in to unmask]]
>> Sent: 18 September 2001 15:28
>> To: [log in to unmask]
>> Subject:
>>
>>
>> Hi.
>>
>> Indeed - although FEAT lets you run lots of first-level analyses from a
>> single setup and push of the "GO" button, you can only do this if the
>> design matrix is the same for all analyses - not the case here.
>>
>> Both of your suggestions are fine, although there are practical downsides
>> to concatenation, so we do not reccomend that in general.
>>
>> Thus - you should carry out each first-level analysis separately. You
>> should obviously make sure that EV1 corresponds to the same stimulus type
>> in each analysis etc. - otherwise second-level analyses will not be able
>> to relate EV1 from session 1 to EV1 in session 2 etc.
>>
>>
>> You can then do simple group stats using FEAT to combine the first-level
>> analyses from the different sessions for a single subject. Note that FEAT
>> cannot yet (though watch this space!) do third-level (etc) analyses so
>> it's not very easy to THEN do group stats across subjects - if you do want
>> to do this, then there is a workaround - a fairly simple way of achieving
>> simplified fixed-effects analyses at any number of levels which we could
>> explain.
>>
>> Thanks, Steve.
>>
>>
>>  Stephen M. Smith
>>  Head of Image Analysis, FMRIB
>>
>>  Oxford University Centre for Functional MRI of the Brain
>>  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>>  +44 (0) 1865 222726  (fax 222717)
>>
>>  [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve
>>
>> On Fri, 7 Sep 2001, Xavier Chitnis wrote:
>>
>> > Dear Steve,
>> >
>> > Thank you very much for your help. I have one more question....
>> >
>> > The task consists of three sessions for each subject. The order of the 4
>> > types of stimuli (ABCD) is different across the three runs. In running one
>> > subject through FEAT, I selected a full first level analysis for 3
>> volumes,
>> > and then selected one session for each volume. However, because the order
>> of
>> > the stimuli is different across the three sessions, I cannot tell FEAT
>> what
>> > the order is for each session, as I think it assumes that they are the
>> same
>> > for each session.
>> >
>> > I have considered two approaches to this. Firstly, to set up and analyse
>> > each session separately. Alternatively, to concatenate the three sessions
>> > into one very large session, and analyse it that way. Is either of these
>> > appropriate, or is there a better way?
>> >
>> > Many thanks
>> >
>> > Xavier
>> >
>> >
>> > -----Original Message-----
>> > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]]On
>> > Behalf Of Stephen Smith
>> > Sent: 06 September 2001 17:23
>> > To: [log in to unmask]
>> > Subject: Re: [FSL] FEAT
>> >
>> >
>> > Aha - good - so in fact all your scanning IS regular, and my initial
>> > worries are gone.
>> >
>> > So - to your original questions:
>> >
>> > >>>>
>> > I set up the analysis (for a single subject as follows). I selected a full
>> > model setup. Given that there are 4 active conditions, I selected 4 EVs.
>> > For the basic shape, I selected Custom (1 entry per volume). I then
>> > created 4 text files, one for each of the active conditions. In each text
>> > file, I used 1 to specify images relating to that active condition, and 0
>> > for every other image.
>> > >>>>
>> >
>> > this is fine - though it might have been easier to simply specify the
>> > activation periods (seconds) for each EV type in 3-column format text
>> > files. the result should be the same.
>> >
>> > >>>>
>> > For the contrasts, I looked for activations in each of the active
>> > conditions (by selecting 1, and 0 for all the others)
>> > >>>>
>> >
>> > this is fine too - and if you want to compare conditions, use [1 -1] type
>> > contrasts.
>> >
>> > Sorry for the confusion - hope it gives the activation you want!
>> >
>> > Thanks, Steve.
>> >
>> >  Stephen M. Smith
>> >  Head of Image Analysis, FMRIB
>> >
>> >  Oxford University Centre for Functional MRI of the Brain
>> >  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>> >  +44 (0) 1865 222726  (fax 222717)
>> >
>> >  [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve
>> >
>>
>> Xavier Chitnis MSc.
>> Division of Psychological Medicine
>> Institute of Psychiatry
>> London, SE5 8AF
>> Tel: 020 7848 0541
>>
>

Top of Message | Previous Page | Permalink

JISCMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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


WWW.JISCMAIL.AC.UK

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