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  

|
January 14, 2021 07:54AM
I've tested the code and this is the output displayed in the Terminal window (below). The resulting rs_errts image looks fine, but I am wondering if additional processing is necessary? For example, executing the 3dREMLfit command?

++ 3dDeconvolve: AFNI version=AFNI_21.0.00 (Jan 7 2021) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ loading dataset rs_f.nii
++ Skipping check for initial transients
++ Input polort=1; Longest run=140.0 s; Recommended minimum polort=1 ++ OK ++
++ Number of time points: 140 (before censor) ; 122 (after)
+ Number of parameters: 11 [10 baseline ; 1 signal]
++ total shared memory needed = 1,018,165,512 bytes (about 1.0 billion)
++ mmap() memory allocated: 1,018,165,512 bytes (about 1.0 billion)
++ Memory required for output bricks = 1,018,165,512 bytes (about 1.0 billion)
++ Wrote matrix values to file rs_all.xmat.1D
++ ========= Things you can do with the matrix file =========
++ (a) Linear regression with ARMA(1,1) modeling of serial correlation:

3dREMLfit -matrix rs_all.xmat.1D -input rs_f.nii \
-mask brainMask_RS.nii.gz -Rbuck rs_all_REML -Rvar rs_all_REMLvar \
-Rfitts rs_fitts_REML -Rerrts rs_errts_REML -verb

++ N.B.: 3dREMLfit command above written to file rs_all.REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
++ ----- Signal+Baseline matrix condition [X] (122x11): 2.28984 ++ VERY GOOD ++
++ ----- Signal-only matrix condition [X] (122x1): 1 ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (122x10): 1.95927 ++ VERY GOOD ++
++ ----- stim_base-only matrix condition [X] (122x8): 1.92574 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (122x2): 1.04606 ++ VERY GOOD ++
++ +++++ Matrix inverse average error = 5.196e-14 ++ VERY GOOD ++
++ Matrix setup time = 0.01 s
++ Voxels in dataset: 902629
++ Voxels in mask: 263820
++ Voxels per job: 131910
++ Job #1: processing voxels 393706 to 902628; elapsed time=2.650
++ Job #0: processing voxels 0 to 393705; elapsed time=2.662
++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789.
++ Job #0 waiting for children to finish; elapsed time=6.085
++ Job #1 finished; elapsed time=6.328
++ Job #0 now finishing up; elapsed time=6.351
++ Smallest FDR q [0 Full_Fstat] = 3.06458e-14
++ Wrote bucket dataset into ./rs_all+tlrc.BRIK
+ created 1 FDR curves in bucket header
++ Wrote 3D+time dataset into ./rs_fitts+tlrc.BRIK
++ Wrote 3D+time dataset into ./rs_errts+tlrc.BRIK
++ Program finished; elapsed time=19.734
Subject Author Posted

3dDeconvolve

Alfonso Alfini January 11, 2021 03:54PM

Re: 3dDeconvolve

Alfonso Alfini January 14, 2021 07:54AM