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  2004

FSL 2004

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Alignment and higher level analysis

From:

Mark Jenkinson <[log in to unmask]>

Reply-To:

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

Date:

Thu, 26 Feb 2004 14:08:19 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (90 lines)

Hi Jane,

I'm afraid you are experiencing the effects of an intermittent
bug in flirt which we think is caused by the compilers we use,
which was unexpected.  What machine are you running it on?
If it is linux (redhat 8 or 9) then a non-optimised version of
flirt, which is slower but doesn't crash, can be installed.
See:
  http://www.fmrib.ox.ac.uk/fslfaq/#flirt_crash

You might need to get your sysadmin to do this for you.

If you are not running on linux/redhat 8 or 9 then let us know.

As for the group analysis, this can happen if there is a lot of
variation between the runs.  Does the data from different runs
appear significantly different in fslview (look at the timeseries)?
Also, if your registrations aren't working then you won't get
any good higher level results.  Do all the registrations in the
registrations reports look good?

If you can't see anything obviously wrong in the above, then let
us know and we can try to have a look at your data/design.

All the best,
    Mark



Jane Aspell wrote:

>Hi
>
>I'm new to FSL and am having a few problems. When I run a first level
>analysis using FEAT for one of my subjects something seems to go wrong with
>the co-registration of the high res image to the standard brain. In Feat
>watcher i get the following error:
>
>/usr/local/fsl/bin/convert_xfm -matonly -inverse -omat standard2highres.mat
>highres2standard.mat
>Could not open matrix file highres2standard.mat
>Cannot read input-matrix
>
>/usr/local/fsl/bin/slicer highres2standard standard -s 1 -x 0.35 sla -x 0.45
>slb -x 0.55 slc -x 0.65 sld -y 0.35 sle -y 0.45 slf -y 0.55 slg -y 0.65 slh
>-z 0.35 sli -z 0.45 slj -z 0.55 slk -z 0.65 sll ; /usr/local/fsl/bin/convert
>-colors 100 +append sla slb slc sld sle slf slg slh sli slj slk sll
>highres2standard.gif ; /bin/rm -f sla slb slc sld sle slf slg slh sli slj
>slk sll
>Cannot open volume highres2standard.hdr for reading!
>convertb: no delegate for this image format (sla).
>convertb: no delegate for this image format (slb).
>convertb: no delegate for this image format (slc).
>convertb: no delegate for this image format (sld).
>convertb: no delegate for this image format (sle).
>convertb: no delegate for this image format (slf).
>convertb: no delegate for this image format (slg).
>convertb: no delegate for this image format (slh).
>convertb: no delegate for this image format (sli).
>convertb: no delegate for this image format (slj).
>convertb: no delegate for this image format (slk).
>convertb: no delegate for this image format (sll).
>convertb: Missing an image file name.
>
>/bin/rm -f highres2standard.hdr highres2standard.img
>
>And I found that the highres2standard.mat transform is missing from the /reg
>directory in the relevant .feat directory.
>So i tried to create it with the command:
>flirt -in highres -ref standard -omat highres2standard.mat
>But that just returns 'Segmentation fault'
>
>I haven't had this problem with my other subject. Any ideas?
>
>My second problem is with higher level analysis. I ran successful first
>level analyses for the 5 series(runs) for a single subject and got good
>activations for my contrasts (z~6) but when i run the higher level analysis
>to put all the runs (which are simply repeats of the same conditions)
>together all the activation seems to disappear! I re-ran the higher level
>analysis with a lower z threshold (1.0) and was then able to see activations
>(z scores <3 could be seen). Is this the correct thing to do? I thought
>the activations would be more significant, not less, when I average all
>my runs together so I'm puzzled.
>
>Thanks very much for your help.
>
>Jane Aspell
>
>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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