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Subject:

Re: 2nd level contrast failure

From:

Tyler Lesh <[log in to unmask]>

Reply-To:

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

Date:

Mon, 22 Mar 2004 18:10:51 +0000

Content-Type:

text/plain

Parts/Attachments:

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text/plain (92 lines)

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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