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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mb
June 06, 2013 01:50PM
I am having a hard time figuring out what the -gltsym command wants in the glt files -- when I search the message board using -glt or -gltsym, it says there are no messages with these words? Anyway, I am getting the following error:

** FATAL ERROR: Can't read GLT matrix from file glt1.txt

Which has the following in it: +Cond1[3..5] -Cond6[3..5] in which Cond1 and Cond6 are defined by -stim_labels. I have modeled this after the example in afni06_decon.pdf, which says the following:

Combining subsets of the β weights is also possible with -gltsym :
+HumanMovie[2..6] -HumanPoint[2..6]
This GLT would add up just the #2,3,4,5, & 6 β weights for one type of stimulus and subtract the sum of the #2,3,4,5, & 6 β weights for another type of stimulus

In3dDeconvolve file:

3dDeconvolve -input r4.scale+orig.HEAD \
-polort A \
-mask skull_mask+orig \
-num_stimts 16 \
-stim_times 1 Cond1.txt 'CSPLIN(0,15,6)' \
-stim_label 1 Cond1 \
-stim_times 2 Cond2.txt 'CSPLIN(0,15,6)' \
-stim_label 2 Cond2 \
-stim_times 3 Cond3.txt 'CSPLIN(0,15,6)' \
-stim_label 3 Cond3 \
-stim_times 4 Cond4.txt 'CSPLIN(0,15,6)' \
-stim_label 4 Cond4 \
-stim_times 5 Cond5.txt 'CSPLIN(0,15,6)' \
-stim_label 5 Cond5 \
-stim_times 6 Cond6.txt 'CSPLIN(0,15,6)' \
-stim_label 6 Cond6 \
-stim_times 7 Cond7.txt 'CSPLIN(0,15,6)' \
-stim_label 7 Cond7 \
-stim_times 8 Cond8.txt 'CSPLIN(0,15,6)' \
-stim_label 8 Cond8 \
-stim_times 9 Cond9.txt 'CSPLIN(0,15,6)' \
-stim_label 9 Cond9 \
-stim_times 10 Cond10.txt 'CSPLIN(0,15,6)' \
-stim_label 10 Other \
-stim_file 11 Motion.1D'[0]' -stim_base 11 -stim_label 11 roll \
-stim_file 12 Motion.1D'[1]' -stim_base 12 -stim_label 12 pitch \
-stim_file 13 Motion.1D'[2]' -stim_base 13 -stim_label 13 yaw \
-stim_file 14 Motion.1D'[3]' -stim_base 14 -stim_label 14 dS \
-stim_file 15 Motion.1D'[4]' -stim_base 15 -stim_label 15 dL \
-stim_file 16 Motion.1D'[5]' -stim_base 16 -stim_label 16 dP \
-jobs 2 \
-gltsym glt1.txt -glt_label 1 C1_C6 \
-bucket stats.GLT

In glt1.txt
+Cond1[3..5] -Cond6[3..5]


thanks, mb
Subject Author Posted

-glt

mb June 06, 2013 01:50PM

Re: -glt

mb June 06, 2013 01:55PM