Hi,
It looks like you are doing this correctly.
How many columns are there in the files ANOVA.mat, mask.mat, ANOVA.con and mask.con?
The first problem needs to be sorted out before you can continue, and I think the information above should help.
Any F-tests can be added to the second randomise call as usual, and should not have changed as a consequence of using setup_masks.
All the best,
Mark
On 13 Feb 2014, at 17:36, Domenico Aquino <[log in to unmask]> wrote:
> Hi all,
>
> I'm conducting an analysis on 3 groups of MS subjects using TBSS.
> I've just done the ANOVA test on the groups, but now I would like to conduct the randomise step removing the lesions.
> I've done what reported in http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/randomise/UserGuide#Associated_Tools (the lesion masking tool), i.e. :
>
>> setup_masks ANOVA.mat ANOVA.con mask sub01.nii sub02.nii sub03.nii sub04.nii sub05.nii sub06.nii sub07.nii sub08.nii sub09.nii sub10.nii sub11.nii sub12.nii sub13.nii sub14.nii sub15.nii sub16.nii sub17.nii sub18.nii sub19.nii sub20.nii sub21.nii sub22.nii sub23.nii sub24.nii sub25.nii sub26.nii sub28.nii sub29.nii sub30.nii sub31.nii sub32.nii sub34.nii sub35.nii sub36.nii sub37.nii sub38.nii sub39.nii sub40.nii sub41.nii sub42.nii sub43.nii sub44.nii sub45.nii sub47.nii sub48.nii sub49.nii sub50.nii sub51.nii sub52.nii sub53.nii sub54.nii sub55.nii sub56.nii sub57.nii sub58.nii sub59.nii sub60.nii sub61.nii sub62.nii sub63.nii
>
> It produces two files: mask.mat and mask.con.
> The second step is to re-launch randomise with these new files:
>
>> randomise -i all_FA_skeletonised.nii -o FA_all_lesions -d mask.mat -t mask.con --vxl=8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67 --vxf=mask_0008,mask_0009,mask_0010,mask_0011,mask_0012,mask_0013,mask_0014,mask_0015,mask_0016,mask_0017,mask_0018,mask_0019,mask_0020,mask_0021,mask_0022,mask_0023,mask_0024,mask_0025,mask_0026,mask_0027,mask_0028,mask_0029,mask_0030,mask_0031,mask_0032,mask_0033,mask_0034,mask_0035,mask_0036,mask_0037,mask_0038,mask_0039,mask_0040,mask_0041,mask_0042,mask_0043,mask_0044,mask_0045,mask_0046,mask_0047,mask_0048,mask_0049,mask_0050,mask_0051,mask_0052,mask_0053,mask_0054,mask_0055,mask_0056,mask_0057,mask_0058,mask_0059,mask_0060,mask_0061,mask_0062,mask_0063,mask_0064,mask_0065,mask_0066,mask_0067 -V --T2
>
> I've two questions:
>
> 1) When I run randomise I obtain the following error "An exception has been thrown
> number of columns in t-contrast matrix doesn't match number of columns in design matrix!". Which could be the problem?
>
> 2) How to conduct an ANOVA analysis, i.e. where to insert the ANOVA.fts file?
>
> Thank you,
>
> Domenico
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