No, you need to use a specific flag for this.From the Randomise User's Guide page:
To use this option, use -c <thresh> for t contrasts and -F <thresh> for F contrasts, where the threshold is used to form supra-threshold clusters of voxels
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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Rosalia Dacosta Aguayo [[log in to unmask]]
Sent: Tuesday, June 25, 2013 10:54 AM
To: [log in to unmask]
Subject: Re: [FSL] TBSS Clustere
Hi Alan,
I think that what do you want to see is if there are statistical significant results in your data.....the name tbss_cluster_corrp_tstat1 is = tbss_corrp_tstat1...the important thing is tfce_corrp....
Best,
Rosalia.
2013/6/25 Alan Francis <[log in to unmask]<mailto:[log in to unmask]>>
Hi Rosalia:
Yes I see the tbss_tfce_corrp_tstat1.nii.g, and tbss_tfce_corrp_tstat2.nii.gz and other files in my output folder. But for some reason I do not see the tbss_clustere_corrp_tstat1. I checked the contrast to see if I have made a mistake. Any ideas?
thank you,
Alan
On Tue, Jun 25, 2013 at 10:42 AM, Rosalia Dacosta Aguayo <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi Alan,
If you have created correctly the design.mat and the design.con files...you should have as outputs: tbss_tfce_corrp_tstat1.nii.gz (for contrast 1) and tbss_tfce_corrp_tstat2.nii.gz (for contrast 2) and so on...depending on the contrasts you have created.. These are the files the practical is referencing as tbss_clustere_corrp_tstat1....
Hope this helps,
Rosalia.
2013/6/25 Alan Francis <[log in to unmask]<mailto:[log in to unmask]>>
Hi FSL folks:
I have been following the Randomize user guide and the FDT and TBSS practical. I ran the following command on 23 brains after creating design.con and design.mat.
randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask \
-d design.mat -t design.con -c 1.5 -V
It generated all the files except the TBSS clustere corrp file. So when I ran the the following command:
fslview $FSLDIR/data/standard/MNI152_T1_1mm mean_FA_skeleton -l Green \
-b .3,.7 tbss_tstat1 -l Red-Yellow -b 1.5,3 tbss_clustere_corrp_tstat1 \
-l Blue-Lightblue -b 0.949,1
it loaded all the files except the cluster. How do I generate the cluster ?
thanks so much,
Alan Francis
Martinos Center
Boston
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