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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Zareal Wang
October 29, 2008 01:02AM
hello, afni experts.
I ran into a problem in GLT test, which is similiar to

[afni.nimh.nih.gov]

Yet, unlike the "row" problem in the above post, I got error in numbers of "columns".

My maxlag is 6, so the matirx should be 4*7+2=30, yet the system said 1*12 is required. I am confused after several tries. Thank you for your help!




The details:
the command I used:
3dDeconvolve -input 043_038_017.1D -num_stimts 4 \
-stim_file 1 stimuli1.1D -stim_label 1 stim1 -stim_minlag 1 0 -stim_maxlag 1 6 \
-stim_file 2 stimuli2.1D -stim_label 2 stim2 -stim_minlag 1 0 -stim_maxlag 1 6 \
-stim_file 3 stimuli3.1D -stim_label 3 stim3 -stim_minlag 1 0 -stim_maxlag 1 6 \
-stim_file 4 stimuli4.1D -stim_label 4 stim4 -stim_minlag 1 0 -stim_maxlag 1 6 \
-glt 1 glta-c.mat -glt_label 1 "a-c" \
-iresp 1 s2all.irf -fitts runall.fit -fout -rout -tout -bucket s2all.bucket

ps: "a-c" means contrast of stim 1 vs stim 3

system reported error as following:

++ 3dDeconvolve: AFNI version=AFNI_2008_07_18_1710 (Oct 23 2008) [32-bit]
++ Authored by: B. Douglas Ward, et al.
++ current memory malloc-ated = 26686 bytes (about 27 thousand)
++ loading dataset 043_038_017.1D
++ current memory malloc-ated = 28510 bytes (about 29 thousand)
*+ WARNING: dataset '043_038_017.1D' has no time axis in its header; cf. 3dinfo
*+ WARNING: no TR in dataset; setting TR=1 s (?)
++ Input polort=1; Longest run=1.0 s; Recommended minimum polort=1 ++ OK ++
Matrix error: In matrix file: glta-c.mat Expected: 1 x 12 Actual: 1 x 30
** Memory usage: chunks=75 bytes=30105
read_glt_matrix
read_input_data
initialize_program
3dDeconvolve main

The content of glta-3.mat:
0 0 1 1 1 1 1 1 1 0 0 0 0 0 0 0 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 0 0 0

info from 3dinfo of input:
[root@localhost s2]# 3dinfo 043_038_017.1D
++ 3dinfo: AFNI version=AFNI_2008_07_18_1710 (Oct 23 2008) [32-bit]

Dataset File: 043_038_017.1D
Identifier Code: A1D_Waff_fqxWI6JXSFI495_aA Creation Date: Wed Oct 29 14:17:04 2008
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: AFNI .1D file
Storage Space: 1800 (1.8 thousand) bytes
Data Axes Tilt: Unspecified, assumed plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: 0.000 -to- 449.000 [L] -step- 1.000 mm [450 voxels]
A-to-P extent: 0.000 -to- 0.000 -step- 1.000 mm [ 1 voxels]
I-to-S extent: 0.000 -to- 0.000 -step- 1.000 mm [ 1 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is float
Subject Author Posted

GLT issue again, please help

Zareal Wang October 29, 2008 01:02AM

Re: GLT issue again, please help

Bob Cox October 29, 2008 07:06AM

Re: GLT issue again, please help

Zareal Wang October 30, 2008 08:48PM