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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