Hello,
Is the mask a standard binary mask? Do you get any extra messages if you add the —debug option?
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 29 May 2017, at 15:47, Darko Komnenić <[log in to unmask]> wrote:
>
> Hello everyone,
> I am a master student using fsl for the first time, so I have some
> questions that might seem trivial. I ran a comparison between two
> groups (patients and controls) using a two-sample unpaired T-test, and
> it worked fine.
> This was my command: randomise -i
> /media/fmriDATA_4/Darko/everyone_lHC.nii -o
> /media/fmriDATA_4/Darko/lHC_test -d /media/fmriDATA_4/Darko.mat -t
> /media/fmriDATA_4/Darko.con -T
>
> My mentor suggested to include a gray matter mask, in order to reduce
> the number of voxels being included in the comparison. I then made
> this command:
> randomise -i /media/fmriDATA_4/Darko/everyone_lHC.nii -o
> /media/fmriDATA_4/Darko/lHC_gmm -d /media/fmriDATA_4/Darko.mat -t
> /media/fmriDATA_4/Darko.con -m
> /media/fmriDATA_4/Darko/masks_HC/mask_j_3.nii -T
>
> but the terminal just remained silent and never started any
> permutation or anything. It seems that the addition of the mask
> somehow glitched it, but when I open the mask file in FSLview, it
> shows a pretty straightforward image of gray matter, so it looks fine.
> Do you maybe have any idea of what might be wrong? Thank you in advance!
> Best regards,
> Darko
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