Hi Celi,

Cluster command is very useful. Use cluster -h for help.

Example to check for 95% significant results in the t-test 1 comparative. Results will be saved in the cluster_t1_95.output file:

cluster -i tbss_tfce_corrp_tstat1.nii.gz -t 0.95 --mm > cluster_t1_95.output

If you have more specific questions about it, do not hesitate to ask me.

Regards,

Alba

Hi Celi,

Cluster command is very useful. Use cluster -h for help.

Example to check for 95% significant results in the t-test 1 comparative. Results will be saved in the cluster_t1_95.output file:

cluster -i tbss_tfce_corrp_tstat1.nii.gz -t 0.95 --mm > cluster_t1_95.output

If you have more specific questions about it, do not hesitate to ask me.

Regards,

Alba

Dear Celi,

for the cluster identification, I also use "cluster" command under FSL.

For the atlas, I usually use the Anatomy toolbox for SPM, that allows me to obtain the clusters in an editable and easy to use format, like txt (I usually import the result file in Excel, and work on that).

In my opinion, it works better then the "atlasquery" command under FSL.

Best Regards,

Sirio

Hello everyone 

i'm a TBSS beginner and i'm wondering  How can i extract FA skeleton value after randomize step on TBSS 

so basically i need to know the FA value of each subject or the mean FA of each group within significant areas highlighted on the skeleton 

thank you beforehand

To Eya: fslmeants from FSL and/or mri_segstats from Freesurfer may help.

I am trying to do that and found this question very helpful. Here is my summary:

1. Use cluster to get an image of cluster indices and a table of p-values and peak as well as center of gravity coordinates.

2. Input the all_FA_skeletonised into fslmeants with the cluster index image as the --label option to get a mean FA per subject per cluster (it will be a matrix of values where rows are subjects and columns are clusters).

Thanks everyone!

Dear All,

I run the full TBSS analysis upto final stage including correction for multiple comparison and observed two tract (left and right) showing significant difference between groups. I want to extract FA value from only one tract for example FA value from right tract.

As per previous posts I can use the command below command:

fslroi

My question is: How can I get the xmin xsize ymin ysize zmin zsize information.