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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Robert Terwilliger
November 18, 2009 04:58PM
Excellent! Worked great.

Okay, so now I'd like to do the same thing but using the CSPLIN basis function set.

Here's deconvolve:
#!/bin/sh

3dDeconvolve \
-input all_float.nii.gz \
-bucket stats \
-concat concat.1D \
-polort 3 \
-num_stimts 14 \
-stim_times 1 congruent_center.1D 'CSPLIN(0,18,7)' \
-stim_label 1 con_center \
-stim_times 2 congruent_cue.1D 'CSPLIN(0,18,7)' \
-stim_label 2 con_cue \
-stim_times 3 congruent_none.1D 'CSPLIN(0,18,7)' \
-stim_label 3 con_none \
-stim_times 4 incongruent_center.1D 'CSPLIN(0,18,7)' \
-stim_label 4 incon_center \
-stim_times 5 incongruent_cue.1D 'CSPLIN(0,18,7)' \
-stim_label 5 incon_cue \
-stim_times 6 incongruent_none.1D 'CSPLIN(0,18,7)' \
-stim_label 6 incon_none \
-stim_times 7 errors.1D 'CSPLIN(0,18,7)' \
-stim_label 7 errors \
-stim_times 8 drops.1D 'CSPLIN(0,18,7)' \
-stim_label 8 drops \
-stim_file 9 'all_mcf.par[0]' -stim_label 9 rx \
-stim_file 10 'all_mcf.par[1]' -stim_label 10 ry \
-stim_file 11 'all_mcf.par[2]' -stim_label 11 rz \
-stim_file 12 'all_mcf.par[3]' -stim_label 12 dx \
-stim_file 13 'all_mcf.par[4]' -stim_label 13 dy \
-stim_file 14 'all_mcf.par[5]' -stim_label 14 dz \
-iresp 1 iresp_congruent_center \
-iresp 2 iresp_congruent_cue \
-iresp 3 iresp_congruent_none \
-iresp 4 iresp_incongruent_center \
-iresp 5 iresp_incongruent_cue \
-iresp 6 iresp_incongruent_none \
-glt 1 alerting.mat -glt_label 1 alerting \
-glt 1 orienting.mat -glt_label 2 orienting \
-glt 1 conflict.mat -glt_label 3 conflict \
-fout \
-rout \
-jobs 2 \
-mask mask.nii.gz \
-GOFORIT 100

##############
error message:
Matrix error: In matrix file: alerting.mat Expected: 1 x 86 Actual: 1 x 38

##############

So, I'm using 7 basis functions. Do I need a column for each basis function?
Subject Author Posted

first time using -glt in 3dDeconvolve

Robert Terwilliger November 18, 2009 04:13PM

Re: first time using -glt in 3dDeconvolve

rick reynolds November 18, 2009 04:35PM

Re: first time using -glt in 3dDeconvolve

Robert Terwilliger November 18, 2009 04:58PM

Re: first time using -glt in 3dDeconvolve

Robert Terwilliger November 18, 2009 05:07PM

Re: first time using -glt in 3dDeconvolve

rick reynolds November 18, 2009 06:03PM

Re: first time using -glt in 3dDeconvolve

Robert Terwilliger November 19, 2009 03:54PM