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.fsf and .fts files are completely different. .fsf stores lots of overall design details and is not needed for randomise. -fts stores F-contrasts. Contrasts are stored in the .con file. Are you doing F-tests or t-tests? If just t-tests (ordinary contrasts) then you don't need the -f or -F options It might be worth reading parts of the FEAT manual to get a better feel for design matrices Cheers, Eugene -- On 27 January 2014 12:26, olof lindberg <[log in to unmask]> wrote: > Hi I sent you the Amir file so that why I put it into the command else my > files have the name > > randomise -i A_Correlatin_left_HC.nii.gz -m > A_Correlatin_left_HC_mask.nii.gz -o Correlation_Amir_L_HC_AGE -d New.mat -t > New.con -f New.fsf --fonly -D -F 3 > > but I not sure I understand how you mean by -f is incorrect - is it the > contence of the .fsf file or should I just not use the -f New.fsf at all > in the command? And in that case how do I then specify my contrast for the > correlation > > I am new beginner so would be a great help if you could explain this! > > > > > 2014-01-27 Eugene Duff <[log in to unmask]> > > The -f input is incorrect: see the input spec - this is meant .fts files >> specifying f-contrasts. Your .mat, .con and .fts files will usually all >> come from the same design spec - why do yours have different names? >> Otherwise OK I think assuming you are not interested in t-tests. >> >> Cheers, >> >> Eugene >> -- >> >> >> On 27 January 2014 12:08, olof lindberg <[log in to unmask]>wrote: >> >>> randomise -i A_Correlatin_left_HC.nii.gz -m >>> A_Correlatin_left_HC_mask.nii.gz -o Correlation_Amir_L_HC_AGE -d Amir.mat >>> -t New.con -f AmirDesign.fsf --fonly -D -F 3 >>> >>> like this i think i tried doing it >>> >>> >>> >>> >>> 2014-01-27 Eugene Duff <[log in to unmask]> >>> >>> Just to be clear: you gave randomise the .fsf file or the .mat file? >>>> Can you give your full command? >>>> >>>> >>>> -- >>>> >>>> >>>> On 27 January 2014 11:54, olof lindberg <[log in to unmask]>wrote: >>>> >>>>> OK, I run the First as usual, just providing a .mat file. >>>>> >>>>> then I want to run correlation analysis with randomise - so I am >>>>> creating the necessary files in glm_gui >>>>> >>>>> I attached this file. >>>>> >>>>> I probably do some simple misstakes but basically I try to input age >>>>> as one EV do see if I have any shape correlation with age >>>>> >>>>> >>>>> 2014-01-27 Eugene Duff <[log in to unmask]> >>>>> >>>>> I'm a bit unclear exactly what you're trying, but design.fsf files are >>>>>> used with FEAT. FIRST itself is for segmentation and doesn't take design >>>>>> matrices (design.mat). >>>>>> >>>>>> Eugene >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> >>>>>> On 27 January 2014 08:44, Olof Lindberg <[log in to unmask]>wrote: >>>>>> >>>>>>> Hi FSL experts. I am trying to run correlation by age in First. I >>>>>>> just put in one EV containing age of subjects in the same order as I >>>>>>> created the concat-file. >>>>>>> >>>>>>> getting: design.fsf is not a valid vest file" when I am trying to >>>>>>> run this >>>>>>> >>>>>>> >>>>>>> what am I doing wrong? >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >