AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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October 25, 2016 07:29PM
Thanks for the advice!

I re-ran this using 3dttest:

3dttest++ -prefix reg_Young_3dttest \
-mask Mask_Young+tlrc \
-covariates Covariates.txt \
-nomeans \
-center NONE \
-setA Subj \
137 /stats.137_PathInt_nt_tcat2+tlrc'[8]' \
143 /stats.143_PathInt_nt_tcat2+tlrc'[8]' \
147 /stats.147_PathInt_nt_tcat2+tlrc'[8]' \
159 /stats.159_PathInt_nt_tcat2+tlrc'[8]' \
...(more subjects)

Subj Perf
137 -1.159
143 -0.682
147 -.047
159 2.655
...(more subjects)

*The Perf values are z-scores.

Sub-brick 8 is the task minus control (block design) t-stat.

I was reading in the other recent message board post "Correlating behavior measures with fmri data" that to get the r-value from the t-score to run:

3dcalc -a reg_Young_3dttest+tlrc[1] \
-expr '(ispositive(a)-isnegative(a))*sqrt(a*a/(a*a+DF))' -prefix corr \

When I look at the initial output (overlay: reg_Young_3dttest: #1 Subj_Perf_Tstat), I am able to see the q value (FDR), but if I look at the output from the 3dcalc (overlay: corr: #0 Subj_Perf_Tstat), the q value is N/A, and there is no longer any significant activity anywhere.

My questions are:
1) With the goal of looking at the correlation between BOLD and performance, is the t-stat: task minus control the correct sub-brick to use? The "Correlating behavior measures with fmri data" also mentioned the need to "standardize" the fMRI data prior to using 3ddtest++, so I wasn't sure if this subbrick was appropriate.
2) If the above procedure was correct, how do I interpret the "disappearance" of significant activity when I convert from t-scores to corr?

Thanks!
Subject Author Posted

Voxel-wise Covariate Only with 3dMVM

usaelzler October 24, 2016 11:04PM

Re: Voxel-wise Covariate Only with 3dMVM

gang October 25, 2016 12:45PM

Re: Voxel-wise Covariate Only with 3dMVM

usaelzler October 25, 2016 07:29PM

Re: Voxel-wise Covariate Only with 3dMVM

gang October 25, 2016 08:58PM