3dDeconvolve Issue with cbucket

AFNI Message Board
1

I tried running 3dDeconvolve with some 1D files, and with the bucket option I was having difficulty understanding the saved output. I saw on the help file that the cbucket command would be better, however, I’m not able to find the output files now. This is what I’ve been doing:

	3dDeconvolve -input1D /$GSR_data_dir/$s/${s}_data.txt						\
		-overwrite										\
		-polort A 										\
		-local_times 										\
		-jobs 4											\
		-num_stimts 6										\
		-concat '1D: 0 319 638 957 1276 1595'							\
		-stim_times 1 $Cond_data_dir/$s/NN.txt 'GAM(8.6, 0.547, 2.0)' -stim_label 1 NN 		\
		-stim_times 2 $Cond_data_dir/$s/PP.txt 'GAM(8.6, 0.547, 2.0)' -stim_label 2 PP 		\
		-stim_times 3 $Cond_data_dir/$s/UU.txt 'GAM(8.6, 0.547, 2.0)' -stim_label 3 UU 		\
		-stim_times 4 $Cond_data_dir/$s/NP_PN.txt 'GAM(8.6, 0.547, 2.0)' -stim_label 4 NP_PN 	\
		-stim_times 5 $Cond_data_dir/$s/NU_UN.txt 'GAM(8.6, 0.547, 2.0)' -stim_label 5 NU_UN 	\
		-stim_times 6 $Cond_data_dir/$s/PU_UP.txt 'GAM(8.6, 0.547, 2.0)' -stim_label 6 PU_UP 	\
		-cbucket /$home_dir/GSR_Deconvolve_output/${s}_betas					\
		-x1D /$home_dir/${s}.x1D

Is there something that’s not compatible with 1D files?

2

As written, the paths to output seem a little
odd. What is $home_dir? I guess if it starts
with ‘/’, the extra one at the beginning does not
actually matter.

You might put an ‘echo’ in front of that command,
and then verify that all of the included directories
actually exist.

It is a little peculiar that you do not also have any
-bucket option. Without it, there are no first level
t-stats, for example.

  • rick
3

Thank Rick,

The bucket option worked.