Hi,
On 8 Oct 2008, at 03:03, Tim Silk wrote:
> Hi Steve,
>
> Thanks for your response. That has been what I was doing.
>
> Below are the errors coming up:
>
> In the Progress Report /log, under higher level analysis, this comes
> up 46 times:
> An exception has been thrown
> Logic error:- detected by Newmat: index error: requested index = 29
>
> MatrixType = Rect # Rows = 28; # Cols = 1
> Trace: Mcmc_Mh::setup; Gsmanager::run.
Exactly which stage of the analysis was this - what analysis were you
trying to carry out at that stage and what was your model?
> Then under Post-stats:
> /usr/local/fsl/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1
Again - what was running at this stage - were you maybe including a
user-specified post-stats mask?
Cheers.
> Image Exception : #3 :: Attempted to multiply images/ROIs of
> different sizes
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> ** ERROR (nifti_image_read): failed to find header file for
> 'thresh_zstat1'
> ** ERROR: nifti_image_open(thresh_zstat1): bad header info
> Error: failed to open file thresh_zstat1
> ERROR: Could not open image thresh_zstat1
> Image Exception : #22 :: Failed to read volume thresh_zstat1
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> while executing
> "exec sh -c " ${FSLDIR}/bin/fslstats thresh_$rawstats -V | awk
> '{ print \$1 }'" "
> (procedure "feat5:proc_poststats" line 93)
> invoked from within
> "feat5:proc_poststats $RERUNNING $STDSPACE "
> ("-poststats" arm line 6)
> invoked from within
> "switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argindex 1
> set session [ lindex $argv $argindex ]
> }
>
> -D {
> incr argindex 1
> set..."
> ("for" body line 2)
> invoked from within
> "for { set argindex 1 } { $argindex < $argc } { incr argindex 1 } {
> switch -- [ lindex $argv $argindex ] {
>
> -I {
> incr argindex 1
> set ses..."
> (file "/usr/local/fsl/bin/feat" line 137)
>
>
>
> Tim
>
>
>
>
>
>
> On Oct 7, 2008, at 11:20 PM, Steve Smith wrote:
>
>> Hi,
>>
>> On 7 Oct 2008, at 08:27, Tim Silk wrote:
>>
>>> Hi,
>>> I am having troubles in the higher level Feat analysis. Each
>>> subject does
>>> 2 sessions, so I run mid-level analysis to combine the sessions.
>>> However, I
>>> have a few subject that completed only 1 session that I want to
>>> include.
>>> Errors occur when I run these subjects in the analysis and no post-
>>> stats
>>> appear.
>>
>> I presume that you are using fixed-effects to combine each
>> subject's first-level results at second level, separately for each
>> subject.
>>
>>> An oddity I have noticed is that even though the registration is
>>> run in the
>>> first level analysis, the report pages show activation displayed on
>>> non-standard brains.
>>
>> This is because first-level analyses are always reported in native
>> space, even though registration has been run (and remembered for
>> later usage).
>>
>>> The report pages for the mid-level analysis show the
>>> activation on a standardised brain (despite no registration
>>> happening at
>>> mid-level).
>>
>> That's right - each subject's second-level fixed-effects analysis
>> will take place in standard space. The registration that had been
>> calculated at first-level is applied at the beginning of the second-
>> level analysis.
>>
>>> I have tried this both adding the .feat directories (with the same
>>> named
>>> copes) as well entering the individual copes.
>>
>> For combining a mixture of first- and second-level analyses at
>> third level, see the FAQ:
>> http://www.fmrib.ox.ac.uk/fslfaq/#feat_mixedup
>> Hopefully this will still work for the latest version of FSL; if
>> not, let us know.
>>
>> Cheers.
>>
>>
>>>
>>>
>>> I hope that makes sense. Please help me work this out.
>>>
>>> Regards,
>>> Tim
>>>
>>
>>
>> ---------------------------------------------------------------------------
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director, Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222726 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>> ---------------------------------------------------------------------------
>
> _____________________________
> Timothy J. Silk, PhD
> NHMRC Research Fellow
> Cognitive and Behavioural Neuroscience
> Queensland Brain Institute
> Brisbane, Australia
>
>
>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR 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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