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Dear AFNI users-

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Sincerely, AFNI HQ

History of AFNI updates  

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March 12, 2022 01:12PM
Hi Afni experts,

I would like to select a stim_times option that can use the trial duration to model both the amplitude AND the width of the HDR.
At this moment, using stim_times_AM1 & 'dmUBLOCK', I can produce ideal stimuli model with HDR amplitude (height) scaled to the trial duration. The trial durations in this design last for 2, 4, and 6 secs.
My two questions are
1). how do I also change the width of the modeled HDR (based on the duration of the trial). -- or you think just modulating the amplitude with the trial duration is good enough!
2). I used the -polort A option and 4 was picked automatically by Afni -- is this the optimal option, why so, and may I have more clarification on the polort function. I read the comprehensive help document of 3dDeconvolve and still struggle to understand. smiling smiley

The rationale of variable epoch comes from Grinband et al., 2008 that both the shape and height of the response in a single short trial will probably vary when the trial duration is a critical variable.
Grinband, J., Wager, T. D., Lindquist, M., Ferrera, V. P., & Hirsch, J. (2008). Detection of time-varying signals in event-related fMRI designs. NeuroImage, 43(3), 509–520. [doi.org]

Here is my 1st level script and please find currently modeled ideal HDR (a comment on the left was used to highlight the four rows of modeled conditions and polort of 2 was tested in this run) and screenshots from Grinband's paper [the 4th blue plot shows as the duration of a short trial increases, the width, height (and slope) of HDR also change (until saturation)]. Please kindly let me know if you notice errors too smiling smiley Thank you!

#!/bin/tcsh
3dDeconvolve -input sub-001_ses-001_task-reward_space-MNI152NLin6Asym_desc-preproc_bold_smooth6_scale.nii -mask sub-001_ses-001_task-reward_space-MNI152NLin6Asym_desc-brain_mask.nii -polort A -num_stimts 20 \
-stim_times_AM1 1 AntLoss.1D 'dmUBLOCK' \
-stim_label 1 AntLoss \
-stim_times_AM1 2 AntMixed.1D 'dmUBLOCK' \
-stim_label 2 AntMixed \
-stim_times_AM1 3 AntNeu.1D 'dmUBLOCK' \
-stim_label 3 AntNeutral \
-stim_times_AM1 4 AntReward.1D 'dmUBLOCK' \
-stim_label 4 AntReward \
-stim_file 5 NuiReg_trans_x.txt'[0]' -stim_base 5 -stim_label 5 trans_x \
-stim_file 6 NuiReg_trans_y.txt'[0]' -stim_base 6 -stim_label 6 trans_y \
-stim_file 7 NuiReg_trans_z.txt'[0]' -stim_base 7 -stim_label 7 trans_z \
-stim_file 8 NuiReg_rot_x.txt'[0]' -stim_base 8 -stim_label 8 rot_x \
-stim_file 9 NuiReg_rot_y.txt'[0]' -stim_base 9 -stim_label 9 rot_y \
-stim_file 10 NuiReg_rot_z.txt'[0]' -stim_base 10 -stim_label 10 rot_z \
-stim_file 11 NuiReg_global_signal.txt'[0]' -stim_base 11 -stim_label 11 global_signal \
-stim_file 12 NuiReg_framewise_displacement.txt'[0]' -stim_base 12 -stim_label 12 framewise_displacement \
-stim_file 13 NuiReg_cosine00.txt'[0]' -stim_base 13 -stim_label 13 NuiReg_cosine00 \
-stim_file 14 NuiReg_cosine01.txt'[0]' -stim_base 14 -stim_label 14 NuiReg_cosine01 \
-stim_file 15 NuiReg_cosine02.txt'[0]' -stim_base 15 -stim_label 15 NuiReg_cosine02 \
-stim_file 16 NuiReg_cosine03.txt'[0]' -stim_base 16 -stim_label 16 NuiReg_cosine03 \
-stim_file 17 NuiReg_cosine04.txt'[0]' -stim_base 17 -stim_label 17 NuiReg_cosine04 \
-stim_file 18 NuiReg_cosine05.txt'[0]' -stim_base 18 -stim_label 18 NuiReg_cosine05 \
-stim_file 19 sub-001_ses-001_task-reward_recording-cardiac_physio_regressors.1D.slibase.1D -stim_base 19 -stim_label 19 phys_resp \
-stim_file 20 sub-001_ses-001_task-reward_recording-respiratory_physio_regressors.1D.slibase.1D -stim_base 20 -stim_label 20 phys_card \
-gltsym 'SYM: AntReward -AntNeutral' \
-glt_label 1 AntRew-AntNeu \
-gltsym 'SYM: AntReward -AntMixed' \
-glt_label 2 AntRew-AntMix \
-gltsym 'SYM: AntReward -AntLoss' \
-glt_label 3 AntRew-AntLoss \
-gltsym 'SYM: AntMixed -AntLoss' \
-glt_label 4 AntMix-AntLoss \
-gltsym 'SYM: AntReward -AntNeutral' \
-glt_label 5 -AntRew_AntNeu \
-gltsym 'SYM: -AntReward AntMixed' \
-glt_label 6 -AntRew_AntMix \
-gltsym 'SYM: -AntReward AntLoss' \
-glt_label 7 -AntRew_AntLoss \
-gltsym 'SYM: -AntMixed AntLoss' \
-glt_label 8 -AntMix_AntLoss \
-ok_1D_text \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.sub-001_ses-001 \
-errts errts.sub-001_ses-001 \
-bucket stats.sub-001_ses-001
Attachments:
open | download - Variable_epoch_HDR.png (86.1 KB)
open | download - 220309_all_regres.jpg (380.2 KB)
Subject Author Posted

3dDeconvolve HDR of variable epoch? (amplitude + duration modulation) Attachments

afni_user_xiy March 12, 2022 01:12PM

Re: 3dDeconvolve HDR of variable epoch? (amplitude + duration modulation)

rick reynolds March 14, 2022 12:02PM

Re: 3dDeconvolve HDR of variable epoch? (amplitude + duration modulation)

afni_user_xiy March 14, 2022 12:50PM

Re: 3dDeconvolve HDR of variable epoch? (amplitude + duration modulation)

rick reynolds March 15, 2022 06:11PM

Re: 3dDeconvolve HDR of variable epoch? (amplitude + duration modulation)

afni_user_xiy March 16, 2022 12:27PM