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

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nic
July 21, 2014 05:40PM
Dear AFNI experts,

I'd like to use TENT functions to estimate the shape of the HRF for a breath-hold (bh) task. My goal is to use bh percent signal change (psc) to scale some task-related psc. Tents are new territory for me ... model specifications below.

Do you have any suggestions as to how many TRs/tent can be censored while still having valid results? TENT vs BLOCK produce the same censor fraction but distributed differently - do I have to pay special attention to this in TENT? I assume there are so many "num TRs per stim" in review.txt bc of tents overlapping. Is there anything especially critical to check with TENT vs other models (aside, of course, from the shape)?

While averaged iresp betas have lost detail of the shape, using those for scaling (vs REML psc) seems somehow more appropriate bc my goal is "reduction of cerebrovascular components" not "detection of regions of sig bh patterns". Would you agree?​

How could I get test statistics for averaged iresp as well as REML betas to threshold these maps and compare to other response models (e.g., BLOCK; sanity/quality check) in a given participant? I have some ideas ... likely more entertaining than proper. A little puzzling: while REML bricks=#tents in the model, iresp bricks=[(42.5-12.5)/(n-2)=2.5], independent of my specification of using only every other interval. Why is that?

WRT above: Paranoidandroid requested the option of unequal tent spacing and I'd like to second that. Bh BOLD is somewhat different from "task BOLD" in that it is more delayed, sluggish, with somewhat pronounced features of varying length – characteristics better modeled with unequal tent spacing, I think.

Sorry about the long post (justifying myself by hoping that it may be helpful for others as well)!

Thank you very much!

Nic


--------------------------------------------------------------------------
Bh task:
6 blocks of 15 sec bh (following a 3 sec countdown)
6 blocks of 27 sec rest
TR=2.5 sec, 115 vols.

Model (locked to every other TR) ... the results look pretty good to me
3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \
-censor censor_${subj}_combined_2.1D \
-polort 2 \
-num_stimts 8 \
-stim_times 1 stimuli/stim_times_breath.1D 'TENTzero(12.5,42.5,8)' \ ... Also estimated 'TENT(12.5,42.5,7)'
-stim_label 1 breath \
-stim_times 2 stimuli/stim_times_breath_instr.1D 'BLOCK(3,1)' \
-stim_label 2 instruction \
-stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll \
-stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch \
-stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw \
-stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS \
-stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL \
-stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP \
-iresp 1 irf \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-errts errts.${subj} \
-bucket stats.$subj
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Subject Author Posted

Re: Question about TENT/SPLIN - number of parameters

nic July 21, 2014 05:40PM

Re: Question about TENT/SPLIN - number of parameters

rick reynolds July 23, 2014 09:54AM

Re: Question about TENT/SPLIN - number of parameters

nic July 23, 2014 06:42PM

Re: Question about TENT/SPLIN - number of parameters

rick reynolds July 24, 2014 04:36PM

Re: Question about TENT/SPLIN - number of parameters

nic July 30, 2014 07:31PM

Re: Question about TENT/SPLIN - number of parameters

nic July 30, 2014 08:58PM

Re: Question about TENT/SPLIN - number of parameters

rick reynolds July 31, 2014 12:38PM

Re: Question about TENT/SPLIN - number of parameters

nic August 10, 2014 07:06PM