Hi,

you could check all the files in the reg_standard directories. A  
quick way of doing this is by using 'slicesdir' which can generate  
summary webpages of registration information

slicesdir -p ${FSLDIR}/etc/standard/avg152T1 filelist

will generate a directory with a webpage containing overlay images  
for every file in filelist against the avg152T1 template. If filelist  
contains all the example_funcs from the reg_standard directory (e.g.  
resampled to standard space) then you can quickly check the quality  
of all registrations in one go... you can do the same for the cope  
images in reg_standard/stats

cheers
christian


On 22 Dec 2006, at 01:42, Katie Karlsgodt wrote:

> Hi,
>   thanks for the suggestion! I actually ended up deleting the  
> reg_standard
> folders, so that featregapply would just get rerun in the gfeat.  
> But, I
> re-ran it and somehow it still isn't right- it still looks like  
> someone has
> a bad mask or there is a big artifact even though they all look  
> normal to me
> (I can tell its a problem with a control subject, because if I run  
> only the
> patient group, it goes fine). Is there anything else I can check,  
> maybe that
> is being fed into the higher level analysis?
> thanks,
> Katie
>
>
>
>> From: Christian Beckmann <[log in to unmask]>
>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>> Date: Thu, 21 Dec 2006 09:04:09 +0000
>> To: <[log in to unmask]>
>> Subject: Re: [FSL] group mask question
>>
>> Hi
>>
>> the images used for higher-level stats are all contained in the
>> reg_standard directory in the original lower-level feat folder. Do
>> these all look OK? If not, you can re-run featregapply ('featregapply
>> blah.feat') to get these files generated.
>> cheers
>> christian
>>
>>
>>
>>
>> On 18 Dec 2006, at 22:06, Katie Karlsgodt wrote:
>>
>>> Hello,
>>>     I'm having a bit of a problem with a group analysis and have
>>> run out of
>>> ideas on how to troubleshoot it. I am re-running an old analysis
>>> from about
>>> a month ago with a slight change. The last time I ran it,
>>> everything was
>>> fine. Now when I run it, the mask looks terrible- as if there is a
>>> really
>>> bad subject in there. I thought maybe one of my files had had a
>>> problem
>>> since I last ran it, so looked at all the subjects registration
>>> pages, which
>>> were fine. I also used slicesdir to look at all the subjects lower
>>> level
>>> masks, tstats, varcope, and mean_func images. I thought it might  
>>> have
>>> somehow had something to do with the change I made (just grouped the
>>> subjects differently), so I just reran the old analysis as it was
>>> before and
>>> the same thing happened. I even thought it might be 3.3 vs 3.2 so
>>> ran the
>>> analysis back in 3.2 again, but it was the same. So I think
>>> something must
>>> be wrong with one of the files, but I can't see which one it is
>>> because
>>> everything I can think of to check is fine... is there some other
>>> way I can
>>> check? or some different files I should be looking for?
>>> thanks!
>>> Katie
>>> ___________________________________
>>> Katie Karlsgodt
>>> Dept of Psychology/Cognitive Neuroscience
>>> University of California, Los Angeles
>>>
>>> [log in to unmask]
>>> phone: (310) 794-9673
>>> fax:   (310) 794-9740
>>
>> --
>>   Christian F. Beckmann
>>   Oxford University Centre for Functional
>>   Magnetic Resonance Imaging of the Brain,
>>   John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>>   Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/ 
>> ~beckmann/
>>   Phone: +44(0)1865 222551 Fax: +44(0)1865 222717
>>
>>

--
  Christian F. Beckmann
  Oxford University Centre for Functional
  Magnetic Resonance Imaging of the Brain,
  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
  Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
  Phone: +44(0)1865 222551 Fax: +44(0)1865 222717