Hi Steve,
So I've actually monitored the analysis up to the point where it fails, and
featregapply appears to be working correctly. It creates all of the
requisite files in the reg_standard folder and I can view them. Also, it
removed the reg_standard folders by itself (even though the avwmerge's
failed). Therefore, every time I have tried to run the analysis, the
reg_standard folder has already been removed.
Thanks,
Tyler
On Sat, 20 Mar 2004 08:42:43 +0000, Stephen Smith <[log in to unmask]>
wrote:
>Hi - this all sounds reasonable. have you tried deleting all of the
>.feat/reg_standard first-level subdirs before running the higher-level
>analysis? If so, did the calls to featregapply from within the
>higher-level run seem to work right?
>
>Cheers, Steve.
>
>
>On Thu, 18 Mar 2004, Tyler Lesh wrote:
>
>> Hi,
>>
>> I've recently run into difficulty performing a 2nd level analysis.
>>
>> I have 14 subjects, with 3 sessions each. I ran the first level, creating
>> feats for each session, registering to the standard template. The second
>> and third levels completed without fail.
>>
>> However, I wanted to redo the analysis using an average brain composed of
>> all of the subjects. I created the average brain according to the FSl
>> tutorial and registered all of the first level feats to this average. (I
>> achieved this by sed-ing the .fsf's and substituting the average brain
for
>> the supplied standard and only running registration.) The registrations
>> look great and I have recently tried to perform a new 2nd level analysis
on
>> these average-registered feat directories.
>>
>> I keep getting this error:
>>
>> no files matched glob pattern "stats0/*hdr"
>> while executing
>> "glob stats0/*hdr "
>> (procedure "feat5:proc" line 883)
>> invoked from within
>> "feat5:proc [ file rootname [ lindex $argv 0 ] ]"
>> (file "/space/raid/fmri/fsl/bin/feat" line 17
>>
>> After viewing the log file, it appears that avwmerge does not
successfully
>> create the merged cope and varcope files and produces this line:
>>
>> /space/raid/fmri/fsl/bin/avwmaths cope1 -mas mask cope1
>> Can't open cope1.hdr
>>
>> and
>>
>> /space/raid/fmri/fsl/bin/avwmaths varcope1 -mas mask varcope1
>> Can't open varcope1.hdr
>>
>> etc.
>>
>> I apologize for the long post, but I have tried manually running
>> featregapply and avwmerge on a single session and it was successful. I
>> have reached the limits of my troubleshooting abilities and am trying to
>> avoid rerunning all of the first level. If anyone has any
recommendations,
>> I would greatly appreciate it.
>>
>> Thanks so much,
>>
>> Tyler
>>
>
> Stephen M. Smith DPhil
> Associate Director, FMRIB and Analysis Research Coordinator
>
> 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
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