Hi - see recent posting on this issue - you can't use contrasts 1 or 2
as permutations of an all-1s EV don't make sense - you need the -1
sign flipping option for testing the mean.
Cheers.
On 25 Nov 2008, at 08:25, Erick Canales Rodriguez (Benito Menni CASM)
wrote:
> Hi Gwenaelle,
>
> My study is in one group of patients, my interest is to test the
> influence of the duration of illness, which is a covariable in the
> analysis (column #2 in design.mat). In addition, Gender was
> considered as a covariable (column #3 in design.mat).
>
> My design.mat:
>
> /NumWaves 3
> /NumPoints 63
> /PPheights 1.000000e+00 3.199000e+03 1.000000e+02
> /Matrix
> 1.000000e+00 -3.960000e+02 2.500000e+01
> 1.000000e+00 -3.960000e+02 2.500000e+01
> 1.000000e+00 -5.960000e+02 -7.500000e+01
> 1.000000e+00 7.030000e+02 -7.500000e+01
> 1.000000e+00 -4.960000e+02 -7.500000e+01
> 1.000000e+00 -1.960000e+02 2.500000e+01
> 1.000000e+00 -1.960000e+02 2.500000e+01
> 1.000000e+00 -9.600000e+01 2.500000e+01
> 1.000000e+00 2.030000e+02 2.500000e+01
> 1.000000e+00 6.030000e+02 -7.500000e+01
> 1.000000e+00 9.030000e+02 -7.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 8.030000e+02 2.500000e+01
> 1.000000e+00 3.000000e+00 2.500000e+01
> 1.000000e+00 -2.960000e+02 -7.500000e+01
> 1.000000e+00 -9.600000e+01 -7.500000e+01
> 1.000000e+00 -6.960000e+02 2.500000e+01
> 1.000000e+00 -3.960000e+02 2.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 -9.600000e+01 2.500000e+01
> 1.000000e+00 -9.600000e+01 2.500000e+01
> 1.000000e+00 1.030000e+02 2.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 -1.960000e+02 2.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 -1.960000e+02 2.500000e+01
> 1.000000e+00 2.030000e+02 2.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 -1.960000e+02 2.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 -3.960000e+02 2.500000e+01
> 1.000000e+00 -1.960000e+02 -7.500000e+01
> 1.000000e+00 9.030000e+02 2.500000e+01
> 1.000000e+00 1.030000e+02 2.500000e+01
> 1.000000e+00 -9.600000e+01 2.500000e+01
> 1.000000e+00 -3.960000e+02 2.500000e+01
> 1.000000e+00 2.303000e+03 2.500000e+01
> 1.000000e+00 -3.960000e+02 -7.500000e+01
> 1.000000e+00 8.030000e+02 2.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 3.030000e+02 -7.500000e+01
> 1.000000e+00 6.030000e+02 -7.500000e+01
> 1.000000e+00 1.030000e+02 -7.500000e+01
> 1.000000e+00 -4.960000e+02 2.500000e+01
> 1.000000e+00 2.030000e+02 2.500000e+01
> 1.000000e+00 6.030000e+02 2.500000e+01
> 1.000000e+00 -1.960000e+02 2.500000e+01
> 1.000000e+00 3.030000e+02 2.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 -8.960000e+02 -7.500000e+01
> 1.000000e+00 -2.960000e+02 -7.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 1.103000e+03 2.500000e+01
> 1.000000e+00 7.030000e+02 2.500000e+01
> 1.000000e+00 -9.600000e+01 2.500000e+01
> 1.000000e+00 -4.960000e+02 2.500000e+01
> 1.000000e+00 2.030000e+02 -7.500000e+01
> 1.000000e+00 1.030000e+02 -7.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 -2.960000e+02 2.500000e+01
> 1.000000e+00 -3.970000e+02 2.500000e+01
> 1.000000e+00 6.030000e+02 2.500000e+01
>
> %%%%%%%%%%%%%%%%%%
>
> My design.con:
>
> /ContrastName1 Hyper-Mean
> /ContrastName2 Hypo-Mean
> /ContrastName3 Hyper-Dur-illness
> /ContrastName4 Hypo-Dur-illness
> /ContrastName5 Hyper-Gender
> /ContrastName6 Hypo-Gender
> /NumWaves 3
> /NumContrasts 6
> /PPheights 1.015611e+00 1.015611e+00 3.221979e+03
> 3.221979e+03 1.050706e+02 1.050706e+02
> /RequiredEffect 0.508 0.508 3.076 3.076 1.208
> 1.208
> /Matrix
> 1.000000e+00 0.000000e+00 0.000000e+00
> -1.000000e+00 0.000000e+00 0.000000e+00
> 0.000000e+00 1.000000e+00 0.000000e+00
> 0.000000e+00 -1.000000e+00 0.000000e+00
> 0.000000e+00 0.000000e+00 1.000000e+00
> 0.000000e+00 0.000000e+00 -1.000000e+00
>
>
> All the best,
>
> Erick J. Canales-Rodríguez
>
> (+34) 93 652 99 99 ext. 255
>
> Unitat de Recerca, Benito Menni CASM (http://www.hospitalbenitomenni.org/Default.aspx
> )
> Sant Boi del Llobregat (Barcelona), Espanya/España/Spain
>
> Benito Menni Complex assistencial en Salut Mental
> ________________________________________
> De: FSL - FMRIB's Software Library [[log in to unmask]] En nombre de
> Gwenaëlle DOUAUD [[log in to unmask]]
> Enviado el: lunes, 24 de noviembre de 2008 15:56
> Para: [log in to unmask]
> Asunto: [FSL] Re : [FSL] FSL-VBM Problem
>
> Hi Erick,
>
> could you please copy/paste the content of your design.mat and
> design.con files?
>
> Cheers,
> Gwenaelle
>
>
> --- En date de : Lun 24.11.08, Erick Canales Rodriguez (Benito Menni
> CASM) <[log in to unmask]> a écrit :
>
>> De: Erick Canales Rodriguez (Benito Menni CASM) <[log in to unmask]
>> >
>> Objet: [FSL] FSL-VBM Problem
>> À: [log in to unmask]
>> Date: Lundi 24 Novembre 2008, 14h52
>> Hello FSL,
>>
>> I am attempting to do a VBM analysis using the instructions
>> from the FSL-VBM v1.1 homepage, however, I am having
>> problems at the last stage of analysis.
>> The script: "fslvbm_3_proc" works properly, it
>> creates the 4D GM images "GM_mod_merg".
>> My problem arise in the last step: "Displaying
>> cluster-based thresholding results". In particular,
>> with the randomise function:
>>
>> randomise -i GM_mod_merg_s3 -m GM_mask -o fslvbm -d
>> design.mat -t design.con -c 2.3 -n 5000 -V
>>
>> It produces all the iterations for the permutation test
>> corresponding to the tstat1 images, which are shown in the
>> linux terminal (for example, 5000 iterations), however, only
>> two iterations are produced for the tstat2 analysis. It
>> seems as if the algorithm was caught in a local minimum at
>> the second iteration.
>>
>> However, with other set of structural data (in the order of
>> 70 subjects) FSL-VBM works fine in my machine...
>>
>> Can anyone tell me how to solve this problem? In aparience
>> all the T1 images used in my study are OK.
>>
>> All the best,
>>
>> Erick J. Canales-Rodríguez
>>
>> (+34) 93 652 99 99 ext. 255
>>
>> Unitat de Recerca, Benito Menni CASM
>> (http://www.hospitalbenitomenni.org/Default.aspx)
>> Sant Boi del Llobregat (Barcelona), Espanya/España/Spain
>>
>> Benito Menni Complex assistencial en Salut Mental
>
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---------------------------------------------------------------------------
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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