Hello,


fslmaths dr_stage3_ic0000_tfce_corrp_tstat1 -thr 0.95 -bin ROI_2functional 

For TFCE explanation it would be better you go to FSL website and look the meaning of randomise and what is TFCE (is a type of correction like FDR = Family Discovery Ratio) to avoid false positives.

Cheers.


2011/8/1 Leslie Engineering <[log in to unmask]>
Hello-

Just for clarification (b/c I don't understand what tfce is and why I would need a dual regression): Basically, I loaded my zstat1_2highres data on top of my anatomical scan. Made a mask over a specific cluster and now would like to threshold so all voxels with p value less than .05 go away. I transformed the mask to functional space and let's say it is now called ROI_2functional. Are you saying I would type the following:

fslmaths ROI_2functional -thr 0.95 -bin NEW

where NEW is the name I give my mask that has now lost all voxels with a p value greater than .05

Is this correct?

Thanks and sorry I don't understand!

On Sun, Jul 31, 2011 at 6:27 PM, Rosalia Dacosta Aguayo <[log in to unmask]> wrote:
Hi Helen

Have you done dual_regression first?

I you have it, you could see than you have a lot of data, the data of interest is (in red) and the threshold is (green)




But, if you have a little sample, like me, and you have results with TFCE you would have to take into account that TFCE corrp is very conservative, so, you may do  the following:

fslmaths dr_stage3_ic0000_tfce_p_tstat1 -thr 0.99 -bin (and the name of your mask).

I hope this helps you more.

Rosalia.


2011/7/31 Leslie Engineering <[log in to unmask]>
I'm sorry I don't understand the values you gave me.

Maybe writing out the command line would help me. For instants, if I want to isolate voxels with a p value .05 or less within a functional ROI mask I made (ex: ROI.nii.gz) I would type the following:

fslmaths ROI.nii.gz -tfce .05 ROI_thresh05.nii.gz

?


On Sun, Jul 31, 2011 at 4:27 PM, Rosalia Dacosta Aguayo <[log in to unmask]> wrote:
I think threshold with TFCE corr.p tstats is 0.95 and with uncorrected results (only TFCE p tstats) is 0.99.

I understand you perfectly, I am naive too, but I am doing this for my work.

I hope this help you.

Rosalia.



2011/7/31 Leslie Engineering <[log in to unmask]>
Hello-

I'm sorry to ask such basic questions, but I am still confused by the threshold option when using fslmaths.

For instants, if I create a mask in anatomical space then transform it to anatomical space and want to threshold for some finite p value would I use fslmaths -thr? 

thanks