 |
 |
Dear Yingying, Thank you very much for your valuable help. I have few more questions and I will be very grateful if you can help/advise: 1) What I was trying to get it was a table with my t-statistic values. 2)Can you please confirm if is correct the fact that: In tbss_tstat1, the intensity value is among 0-3, and FA of controls is > significant higher than patients in the voxels where intensity is between 0-0.05 while in tbss_tstat2, the intensity value is also among 0-3, FA of > patients is significant higher than > controls in the voxels where intensity is between 0-0.05? I have 30 controls and 32 patients and the way I defined up my matrices is as you can see in the attached files: design.mat and design.con (I saved them for you in a .txt format so you can open them). While checking with imglob *_FA.* I saw first the controls files then the patients files so in the desing.mat I wrote first my controls with 0 in the first column and 1 in the second column and the I added the patients with 1 and the 0 in the second column. 3) After I ran the randomise: design_ttest2 design 30 32 randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 5000 --T2 -V I don't understand why my matrix changed. If I open now after randomise my design. mat I see first patients with 1 and 0 the controls with 0 and 1. Can you please explain how this is possible? 4) If I visualize the UNTHRESHOLDED t-stats results what's the meaning of the values that comes after -b: fslview $FSLDIR/data/standard/MNI152_T1_1mm mean_FA_skeleton -l Green -b 0.2,0.8 tbss_tstat1 -l Red-Yellow -b 3,6 tbss_tstat2 -l Blue-Lightblue -b 3,6 I suppose is a threshold only for data visualization or is something else. I saw some people use 1.3,3 instead of 3, 6. Can you pleases explain? Which one is the best to be used? 5) When I check my corrected p-value image: 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 0.9,1 the only clusters which survived is for a 0.9 threshold. In this case I got two clusters with Z-max = 0.913. Is this value equal with 1-p so in this case the p value for the two clusters will be 0.087? How is possible to get the same p value for both clusters? I suppose this clusters are not significant statistically since >0.05. Am I right? Thank you very much for your time and help. Best regards,Antonella Date: Fri, 4 Nov 2011 01:34:25 -0400 From: [log in to unmask] Subject: Re: [FSL] t statistics To: [log in to unmask] Hi Antonella, From this command you wrote, you will have the t-map as well. Look at the folder. It should have files named tbss_tstats... Depends on your contrasts ... For eg, if you have two contrasts (1,2), you will see six files after you run: randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 5000 --T2 -V tbss_tfce_corrp_tstat1.nii.gz -- corrected p value tbss_tfce_corrp_tstat2.nii.gz -- corrected p value tbss_tfce_p_tstat1.nii.gz -- uncorrected p value tbss_tfce_p_tstat2.nii.gz -- uncorrected p value for contrast 2 tbss_tstat1.nii.gz -- t value for contrast 1 -- that's what you wanted tbss_tstat2.nii.gz -- t value for contrast 2 you can use following command lines to get the significant t map: steps (1) fslmaths tbss_tfce_corrp_tstat1.nii.gz -thr 0.95 tbss_tfce_corrp_tstat1_th95 (2) fslmaths tbss_tstat1.nii.gz -mas tbss_tfce_corrp_tstat1_th95 tbss_tstat1_masked If you want to know the x,y,z for your corrected map. (3) cluster -i tbss_tfce_corrp_tstat1.nii.gz -t 0.95 --mm Hope these are helpful to you. Cheers, Yingying =========================================================== Yingying Wang, Graduate Student, Biomedical Engineering, University of Cincinnati. Pediatric Neuroimaging Research Consortium, Cincinnati Children's Hospital Medical Center. MLC 5033, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, United States. O: 513-636-3495 C: 513-833-7448 Email: [log in to unmask] Blog: http://wang2yg.blogspot.com Homepage: http://homepages.uc.edu/~wang2yg =========================================================== >>> antonella torok <[log in to unmask]> 11/3/2011 4:44 PM >>> Dear FSL experts, Is theer a way to get the t statistics values in significant clusters from my TFCE results? For TFCE I was using the following command: design_ttest2 design 30 32 randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 5000 --T2 -V Thank you for your time and your valuable support. Best regards, Claudia ------------------------------ Antonella Kis, PhD Research Fellow Department of Life Sciences University of Toronto at Scarborough Phone: 416-208-4869 Fax: 416-287-7642