Stim File Errors with 3ddeconvolve

chays · November 8, 2017, 9:25pm

I am having trouble getting AFNI to read my stimfiles for 3ddeconvolve. After running the script I get the following error:

*+ WARNING: ‘-stim_times 1’ didn’t read any good times from file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.EWO.1D’
*+ WARNING: ‘-stim_times 2’ didn’t read any good times from file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.SWOF.1D’
*+ WARNING: ‘-stim_times 3’ didn’t read any good times from file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.EWOC.1D’
*+ WARNING: ‘-stim_times 4’ didn’t read any good times from file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.SWO.1D’
*+ WARNING: ‘-stim_times 5’ didn’t read any good times from file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.EWOF.1D’
*+ WARNING: ‘-stim_times 6’ didn’t read any good times from file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.SWOC.1D’
++ 3dDeconvolve: AFNI version=AFNI_17.2.16 (Jul 8 2015) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ current memory malloc-ated = 330,260 bytes (about 330 thousand [kilo])
++ loading dataset TG_B7_20170608.lex.allruns.blurTo6.scale+tlrc.
++ current memory malloc-ated = 743,788,529 bytes (about 744 million [mega])
++ Skipping check for initial transients
++ Input polort=3; Longest run=305.0 s; Recommended minimum polort=3 ++ OK ++
++ -stim_times using TR=2.5 s for stimulus timing conversion
++ -stim_times using TR=2.5 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise
+ WARNING: -stim_times 1 has all times equal to '’ ?!?!
++ ** GUESSED ** -stim_times 1 using GLOBAL times
+ WARNING: ‘-stim_times 1’ (GLOBAL) has 6 '’ fillers; do you want LOCAL times?
*+ WARNING: !! ‘-stim_times 1’ file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.EWO.1D’ has no good stimulus time values
+ WARNING: -stim_times 2 has all times equal to '’ ?!?!
++ ** GUESSED ** -stim_times 2 using GLOBAL times
+ WARNING: ‘-stim_times 2’ (GLOBAL) has 6 '’ fillers; do you want LOCAL times?
*+ WARNING: !! ‘-stim_times 2’ file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.SWOF.1D’ has no good stimulus time values
+ WARNING: -stim_times 3 has all times equal to '’ ?!?!
++ ** GUESSED ** -stim_times 3 using GLOBAL times
+ WARNING: ‘-stim_times 3’ (GLOBAL) has 6 '’ fillers; do you want LOCAL times?
*+ WARNING: !! ‘-stim_times 3’ file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.EWOC.1D’ has no good stimulus time values
+ WARNING: -stim_times 4 has all times equal to '’ ?!?!
++ ** GUESSED ** -stim_times 4 using GLOBAL times
+ WARNING: ‘-stim_times 4’ (GLOBAL) has 6 '’ fillers; do you want LOCAL times?
*+ WARNING: !! ‘-stim_times 4’ file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.SWO.1D’ has no good stimulus time values
+ WARNING: -stim_times 5 has all times equal to '’ ?!?!
++ ** GUESSED ** -stim_times 5 using GLOBAL times
+ WARNING: ‘-stim_times 5’ (GLOBAL) has 6 '’ fillers; do you want LOCAL times?
*+ WARNING: !! ‘-stim_times 5’ file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.EWOF.1D’ has no good stimulus time values
+ WARNING: -stim_times 6 has all times equal to '’ ?!?!
++ ** GUESSED ** -stim_times 6 using GLOBAL times
+ WARNING: ‘-stim_times 6’ (GLOBAL) has 6 '’ fillers; do you want LOCAL times?
*+ WARNING: !! ‘-stim_times 6’ file ‘/data/T32/Gollan_LexSwitch/LEX_logfiles/TG_B7_20170608.lex.SWOC.1D’ has no good stimulus time values

My stim files look like this currently:

15 *
105
60
195
150
240

I added the asterisk to the first stim time so that it was not mistaken for global time. Do I need to add an asterisk after each stim time? I have 6 runs and there is exactly one stimulus per run? I also used the file_tool -test -infile command and got the following for each of the 6 stim files:

TG_B7_20170608.lex.SWO.1D has 0 bad characters

TG_B7_20170608.lex.SWO.1D file type: UNIX

Any help would be greatly appreciated!

-Chelsea

rickr · November 9, 2017, 1:54pm

Hi Chelsea,

What is the output of this?

timing_tool.py -multi_timing TG_B7_20170608.lex.*.1D
-multi_timing_to_event_list GE:ALL -

Also, what about file_tool?

file_tool -test -infiles TG_B7_20170608.lex.*.1D

rick

chays · November 9, 2017, 7:57pm

Thanks so much for your help with this. Here is the output from the commands you gave me:

[chays@induction LEX_logfiles]$ timing_tool.py -multi_timing TG_B7_20170608.lex.*.1D -multi_timing_to_event_list GE:ALL -

have 6 events in run 1

class prev_class event_time timediff duration stim_file

1 INIT 15.000 15.000 0.000 TG_B7_20170608.lex.EWO.1D
6 1 60.000 45.000 0.000 TG_B7_20170608.lex.SWOF.1D
2 6 105.000 45.000 0.000 TG_B7_20170608.lex.EWOC.1D
4 2 150.000 45.000 0.000 TG_B7_20170608.lex.SWO.1D
3 4 195.000 45.000 0.000 TG_B7_20170608.lex.EWOF.1D
5 3 240.000 45.000 0.000 TG_B7_20170608.lex.SWOC.1D

have 6 events in run 2

class prev_class event_time timediff duration stim_file

6 INIT 15.000 15.000 0.000 TG_B7_20170608.lex.SWOF.1D
4 6 60.000 45.000 0.000 TG_B7_20170608.lex.SWO.1D
1 4 105.000 45.000 0.000 TG_B7_20170608.lex.EWO.1D
5 1 150.000 45.000 0.000 TG_B7_20170608.lex.SWOC.1D
2 5 195.000 45.000 0.000 TG_B7_20170608.lex.EWOC.1D
3 2 240.000 45.000 0.000 TG_B7_20170608.lex.EWOF.1D

have 6 events in run 3

class prev_class event_time timediff duration stim_file

2 INIT 15.000 15.000 0.000 TG_B7_20170608.lex.EWOC.1D
1 2 60.000 45.000 0.000 TG_B7_20170608.lex.EWO.1D
3 1 105.000 45.000 0.000 TG_B7_20170608.lex.EWOF.1D
6 3 150.000 45.000 0.000 TG_B7_20170608.lex.SWOF.1D
5 6 195.000 45.000 0.000 TG_B7_20170608.lex.SWOC.1D
4 5 240.000 45.000 0.000 TG_B7_20170608.lex.SWO.1D

have 6 events in run 4

class prev_class event_time timediff duration stim_file

4 INIT 15.000 15.000 0.000 TG_B7_20170608.lex.SWO.1D
5 4 60.000 45.000 0.000 TG_B7_20170608.lex.SWOC.1D
6 5 105.000 45.000 0.000 TG_B7_20170608.lex.SWOF.1D
3 6 150.000 45.000 0.000 TG_B7_20170608.lex.EWOF.1D
1 3 195.000 45.000 0.000 TG_B7_20170608.lex.EWO.1D
2 1 240.000 45.000 0.000 TG_B7_20170608.lex.EWOC.1D

have 6 events in run 5

class prev_class event_time timediff duration stim_file

3 INIT 15.000 15.000 0.000 TG_B7_20170608.lex.EWOF.1D
2 3 60.000 45.000 0.000 TG_B7_20170608.lex.EWOC.1D
5 2 105.000 45.000 0.000 TG_B7_20170608.lex.SWOC.1D
1 5 150.000 45.000 0.000 TG_B7_20170608.lex.EWO.1D
4 1 195.000 45.000 0.000 TG_B7_20170608.lex.SWO.1D
6 4 240.000 45.000 0.000 TG_B7_20170608.lex.SWOF.1D

have 6 events in run 6

class prev_class event_time timediff duration stim_file

5 INIT 15.000 15.000 0.000 TG_B7_20170608.lex.SWOC.1D
3 5 60.000 45.000 0.000 TG_B7_20170608.lex.EWOF.1D
4 3 105.000 45.000 0.000 TG_B7_20170608.lex.SWO.1D
2 4 150.000 45.000 0.000 TG_B7_20170608.lex.EWOC.1D
6 2 195.000 45.000 0.000 TG_B7_20170608.lex.SWOF.1D
1 6 240.000 45.000 0.000 TG_B7_20170608.lex.EWO.1D

[chays@induction LEX_logfiles]$ file_tool -test -infiles TG_B7_20170608.lex.*.1D
TG_B7_20170608.lex.EWO.1D has 0 bad characters

TG_B7_20170608.lex.EWO.1D file type: UNIX
TG_B7_20170608.lex.EWOC.1D has 0 bad characters

TG_B7_20170608.lex.EWOC.1D file type: UNIX
TG_B7_20170608.lex.EWOF.1D has 0 bad characters

TG_B7_20170608.lex.EWOF.1D file type: UNIX
TG_B7_20170608.lex.SWO.1D has 0 bad characters

TG_B7_20170608.lex.SWO.1D file type: UNIX
TG_B7_20170608.lex.SWOC.1D has 0 bad characters

TG_B7_20170608.lex.SWOC.1D file type: UNIX
TG_B7_20170608.lex.SWOF.1D has 0 bad characters

TG_B7_20170608.lex.SWOF.1D file type: UNIX

I also forgot to mention that after running 3ddeconvolve (and getting errors associated with the stimulus timing files) the stimulus times all get replaced with astericks. For example, the stim files will then all read like this after trying to run 3ddeconvolve:

Best,

Chelsea

rickr · November 9, 2017, 8:25pm

Hi Chelsea,

All of that output looks good to me.

It is strange to imagine 3dDeconvolve overwriting those
files. But whatever is happening with that seems like a
likely culprit for the overall problem.

Are you able to email me a .tgz package that includes the
timing files and your processing script? Click on my name
for my email address.

rick

chays · November 9, 2017, 9:13pm

Hi Rick,
I just sent the file, but it was still too large for emailing (it included a data file) so I believe it will arrive via googledoc. I also sent another email from another email address that includes only the script and timing files so that one should go through properly. Please let me know if you don’t get the data or if you need anything else. I appreciate your help!

Chelsea

chays · November 13, 2017, 7:13pm

Hi Rick. I just wanted to follow up! Did you receive the email with the script and timing files? Thanks so much for your help with this.

Best,

Chelsea

chays · November 13, 2017, 8:29pm

Hi Rick. So I opened some old stim files that were running properly with the same script on a prior analysis and then edited those with the same format and now they work. Not sure what was going on. When I run the file_tool test command… they looked identical so maybe there was some sort of an error that was happening in the original text files that was not being picked up by the debugging command. Anyways, thank you for your help and I am glad that it is now fixed! Have a great week.

rickr · November 13, 2017, 10:03pm

Sorry for being slow. I did get them and saw no problems,
so I was waiting for more time to investigate further. It is
good to know things are working!

rick