Dear Andrade,
I am assuming ( from the commands listed ) you are at stage E of FSLVBM:
1) Your fslmaths call ( fslmaths GM_mod_merg -s 3.5 GM_mod_merg_s3.5 ) implies that you have chosen a custom value (sigma 3.5mm) for smoothing your data, but your randomise call ( randomise -i GM_mod_merg_s3 -m GM_mask -o fslvbm -d design.mat -t design.con -T -n 5000 ) is taking the standard 3mm smoothed input. This is inconsistent but fine if the 3mm results are the ones you wish to generate stats for.
2) The outputs from randomise will be of the form fslvbm_<foo> ( e.g. fslvbm_tfce_corrp_tstat1.nii.gz ) and these are the images you probably want to view in fsleyes/fslview as well as run cluster on ( presuming you want a cluster-table ).
An example cluster call could be
cluster -i fslvbm_tfce_corrp_tstat1 -t 0.95
using a significance level of 0.05 ( as randomise output 1-p images ).
The above command will output voxel co-ordinates for the cluster maxima etc, this can be switched to mm with the --mm option.
Hope this helps,
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 8 Sep 2019, at 21:45, Renew Andrade <[log in to unmask]> wrote:
>
> Dear experts:
>
> I am on my way to interpret the results of FSL VBM and I am doing my cluster part.
>
> I write
>
>
> cluster -i GM_mod_merg_s2_tstat1.nii.gz -t 2.5 -o cluster_index_s2_1 --osize=cluster_size_s2_1 > cluster_info_s2_1.txt
>
> But I am not sure of the results because all the coordinates are positive and of course the atlasquery would give me disparate results the vast majority is unknown and or pretty much the same areas in the brain.
>
> I copied from
>
> cluster -i myinputimage -t 2.5 -o cluster_index --osize=cluster_size > cluster_info.txt
>
>
> I do not know if myinputimage is any *tstat*.nii.gz file.
>
> Thanks for the help!
>
> Sincerely,
> Andrade.
>
> PD I forgot to mention in the processing stream I did
>
> fslmaths GM_mod_merg -s 3.5 GM_mod_merg_s3.5
>
>
> after this
>
> randomise -i GM_mod_merg_s3 -m GM_mask -o fslvbm -d design.mat -t design.con -T -n 5000
>
> I do not know if that is relevant and in that case how to fix it probably deleting output files from randomise and re-run from fslvbm_3_proc
>
>
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