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Hi , Can I use the "cluster" command to report the peak of the clusters in the randomise with t-stat ? Is it right to use the following command ? cluster -i tbss_tfce_corrp_tstat1 -t 0.95 -c tbss_tstat1 --scalarname="1-p" > cluster_corrp1.txt And I don't understand the words " do not base the clusters on the t-stat, but run the cluster command using the corrp image as the input and -t 0.95 (in which case you don't need to run the first fslmaths command either) " in your reply . Best . Xinfa Shi . 2014-06-04 14:27 GMT+08:00 Mark Jenkinson <[log in to unmask]>: > Hi, > That version is quite old now so we recommend you upgrade to the latest > version. The old version is definitely the cause of the problem you are > having with the --scalarname option. > All the best, > Mark > On 4 Jun 2014 01:59, Xinfa Shi <[log in to unmask]> wrote: > Hi ， > > I‘m using FSL 4.1.9 .Is there a problem ? > > Best . > > Xinfa Shi . > > > 2014-06-04 3:02 GMT+08:00 Anderson M. Winkler <[log in to unmask]>: > >> Hi Xinfa, >> Not sure... Maybe you are using an old version of FSL? >> Anderson >> >> >> >> On 3 June 2014 16:07, Xinfa Shi <[log in to unmask]> wrote: >> >>> Hi , >>> To report cluster information from randomise output t-test , could I >>> use the following command : >>> cluster -i tbss_tfce_corrp_tstat1 -t 0.95 -c tbss_tstat1 >>> --scalarname="1-p" > cluster_corrp1.txt >>> >>> I try it ,but the error message occur : --scalarname: Option doesn't >>> exist >>> Why ? >>> >>> Best . >>> >>> Xinfa Shi . >>> >>> >>> >>> 2014-05-31 19:16 GMT+08:00 Anderson M. Winkler <[log in to unmask]>: >>> >>> >>> PS: oops! where I wrote z-stat I meant t-stat, the image that you are >>>> using with -mul in fslmaths. Regardless, you already got other insights >>>> from MJ! >>>> >>>> >>>> Am 30/05/2014 23:58, schrieb Anderson M. Winkler: >>>> >>>> Hi Xinfa, >>>> >>>> The procedure to get the coordinates looks fine to me. >>>> Regarding the difference, it might be that you are using the TFCE >>>> image in FSLview, whereas the peak of the clusters is being identified with >>>> the z-stat image; they aren't guaranteed to be the same, and will often >>>> differ: TFCE has the benefit if considering also the spatial extent, >>>> something the simple z-stat doesn't do. >>>> >>>> All the best, >>>> >>>> Anderson >>>> >>>> >>>> >>>> On 29 May 2014 15:11, SUBSCRIBE FSL Xinfa_Shi < >>>> [log in to unmask]> wrote: >>>> >>>>> Hi , >>>>> >>>>> Now I have finished statistic analysis about FA data in TBSS by the >>>>> command “randomise “, getting these files( tbss_tstat1.nii.gz , >>>>> tbss_tstat2.nii.gz, tbss_tfce_corrp_tstat1.nii.gz , >>>>> tbss_tfce_corrp_tstat2.nii.gz , tbss_tfce_p_tstat1.nii.gz , and >>>>> tbss_tfce_p_tstat2.nii.gz) . Then I want to sort out the result following >>>>> the steps below ： >>>>> 1. Getting Cluster and Peak Information from Randomise Output by >>>>> following commands: >>>>> fslmaths tbss_tfce_corrp_tstat1 -thr 0.90 -bin -mul tbss_tstat1 >>>>> tbss_thresh_tstat1 >>>>> >>>>> cluster --in=tbss_thresh_tstat1 --thresh=0.0001 >>>>> --oindex=tbss_cluster_index --olmax=tbss_lmax.txt --osize=tbss_cluster_size >>>>> >>>>> The result is : >>>>> Cluster Index Voxels Z-MAX Z-MAX X (mm) Z-MAX Y (mm) >>>>> Z-MAX Z (mm) Z-COG X (mm) Z-COG Y (mm) Z-COG Z (mm) >>>>> 6 2077 4.11 46 26 9 33.7 10.2 22.2 >>>>> 5 1190 4.68 -20 23 35 -22.3 29.2 18.4 >>>>> 4 850 3.55 19 3 41 15.8 17.6 32.8 >>>>> 3 104 3.99 21 46 3 18.9 41.3 -2.34 >>>>> 2 58 3.12 32 -34 13 30.9 -35.2 15.1 >>>>> 1 46 4.47 30 18 37 30.3 17.9 37.4 >>>>> >>>>> 2. View tbss_tfce_corrp_tstat1 loading the white matter atlas >>>>> JHU-WhiteMatter-labels-1mm.nii.gz in fslview by the following command: >>>>> >>>>> fslview $FSLDIR/data/standard/MNI152_T1_1mm mean_FA_skeleton -l Green >>>>> -b 0.2,0.7 tbss_tfce_corrp_tstat1 -l Red-Yellow -b 0.90,1 >>>>> The result is seen in the attached picture . >>>>> >>>>> Question: >>>>> >>>>> 1. Is it right in the above process ? >>>>> 2. In FSLView , the coordinates (mm) presenting significant >>>>> difference (Red-Yellow) are different from the coordinates (mm) deriving >>>>> from cluster command . >>>>> That’s why ? What is the relation between them ? >>>>> >>>>> Maybe my expression is not clear due to poor English ,and I’m very >>>>> sorry for it . >>>>> In a word ,I want to know that how should I sort out the result >>>>> presenting brain regions and clusters . >>>>> >>>>> Best . >>>>> >>>>> Xinfa Shi. >>>>> >>>>> >>>>> >>>> >>>> >>> >> >