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  

Previous Message Next Message
Message List New Topic Print View
|
nstuart
November 07, 2019 12:51PM
Hello,

I'm having trouble with the script (which is the following): 
3dDeconvolve -force_TR 2 -input scaled_allruns+orig -mask retrieval_mask+orig -concat '1D: 0 60 120 180 240 300' \
-polort 1 \
-num_stimts 4 \
-stim_times 1 stimtimes_list.txt 'BLOCK(2,1)' \
-stim_times 2 stimtimes_write.txt 'BLOCK(2,1)' \
-stim_times 3 stimtimes_draw.txt 'BLOCK(2,1)' \
-stim_times 4 stimtimes_new.txt 'BLOCK(2,1)' \
-stim_label 1 write_tar \
-stim_label 2 list_tar \
-stim_label 3 draw_tar \
-stim_label 4 new_tar \
-gltsym 'SYM: draw_tar -write_tar' \
-gltsym 'SYM: draw_tar -list_tar' \
-gltsym 'SYM: draw_tar -new_tar' \
-gltsym 'SYM: list_tar -write_tar' \
-gltsym 'SYM: list_tar -new_tar' \
-gltsym 'SYM: write_tar -new_tar' \
-glt_label 1 draw_write \
-glt_label 2 draw_list \
-glt_label 3 draw_new \
-glt_label 4 list_write \
-glt_label 5 list_new \
-glt_label 6 write_new \
-fitts fitts_event \
-fout -tout -rout -bucket decon_sa_event \
-x1D X.xmat.1D -xjpeg X.jpg


This is the error I am getting: 
** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise
++ ** GUESSED ** -stim_times 1 using LOCAL times
*+ WARNING: '-stim_times 1' (LOCAL) run#6 has 5 times outside range 0 .. -2 [PSFB syndrome]
 + dataset TR being used is 2 s -- unusable times follow
 6 16 26 47 81
++ ** GUESSED ** -stim_times 2 using LOCAL times
*+ WARNING: '-stim_times 2' (LOCAL) run#6 has 4 times outside range 0 .. -2 [PSFB syndrome]
 + dataset TR being used is 2 s -- unusable times follow
 33 37 53 72
++ ** GUESSED ** -stim_times 3 using LOCAL times
*+ WARNING: '-stim_times 3' (LOCAL) run#6 has 5 times outside range 0 .. -2 [PSFB syndrome]
 + dataset TR being used is 2 s -- unusable times follow
 19 42 63 90 103
++ ** GUESSED ** -stim_times 4 using LOCAL times
*+ WARNING: '-stim_times 4' (LOCAL) run#6 has 14 times outside range 0 .. -2 [PSFB syndrome]
 + dataset TR being used is 2 s -- unusable times follow

 11 40 61 67 69 74 85 87 92 98 100 109 114 118
------------------------------------------------------------
GLT matrix from 'SYM: draw_tar -write_tar':

   0   0   0   0   0   0   0   0   0   0   0   0  -1   0   1   0 
------------------------------------------------------------
GLT matrix from 'SYM: draw_tar -list_tar':

   0   0   0   0   0   0   0   0   0   0   0   0   0  -1   1   0 
------------------------------------------------------------
GLT matrix from 'SYM: draw_tar -new_tar':

   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1  -1 
------------------------------------------------------------
GLT matrix from 'SYM: list_tar -write_tar':

   0   0   0   0   0   0   0   0   0   0   0   0  -1   1   0   0 
------------------------------------------------------------
GLT matrix from 'SYM: list_tar -new_tar':

   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0  -1 
------------------------------------------------------------
GLT matrix from 'SYM: write_tar -new_tar':

   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0  -1 


** FATAL ERROR: 3dDeconvolve dies: Invalid -concat input: 300 

** Program compile date = Sep 13 2019



One thing to note is that there is a row that has an asterisk (*) in the txt file, as there was an error when recording that block so I am excluding the stimtimes for that block.
Reply Quote
RSS
Subject Author Posted

3dDeconvolve script error

nstuart November 07, 2019 12:51PM

Re: 3dDeconvolve script error

rick reynolds November 14, 2019 08:23PM