Hi,
On 9 Oct 2008, at 00:42, Tim Silk wrote:
> Steve,
>
> I have two groups (A & B) with 15 subjects in each group. Each
> subject has a different event-related model base on correct and
> incorrect responses. All first level-analysis looks as though it
> worked well.
> Then at mid-level analysis, the 2 session blocks that subjects did
> were combined, except 2 subjects which we only got 1 session block
> for. Mid-level analysis was done using fixed effects.
>
> So for the higher-level analysis, I have tried both entering lower
> level Feat directories and individual 3D copes.
Do you mean that you entered a mix of lower-level FEAT directories and
3D copes, or you tried running FEAT both ways? I would think that you
should only try entering 3D copes, and enter those explicitly from
inside the stats subdirectories in each of the 1st or 2nd level
subject analyses. Maybe this is what you already tried?
Cheers.
> I have the number of inputs as 30, and using the model set up
> wizard, select the two groups unpaired model, and use Flame 1 + 2.
> There is no post stats mask. Having done this, I press Go. The web
> browser pops up and starts running. When I come back to it, it
> appears to have finished, but nothing appears under the post-stats
> tab and in the log file the below error messages occur.
>
> Note: When I do all the above, but remove the 2 subject that only
> have 1 session, so there is 15 subjects in one group and 13 in the
> other, it works fine.
>
> Cheers
>
>
>
>
>
> On Oct 8, 2008, at 6:24 PM, Steve Smith wrote:
>
>> 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
>> ---------------------------------------------------------------------------
>
> _____________________________
> 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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