3dbucket error

AFNI Message Board
1

Hi,

I would like to extract beta weights using 3dbucket command but I’m getting this error:

3dbucket -prefix sub03_betas stats.sub03+orig’[1…73(3)]’
Badly placed ()'s.

Then I tried this:

3dbucket -prefix sub03_betas stats.sub03+orig’[1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70 73]’
++ 3dbucket: AFNI version=AFNI_19.0.07 (Feb 5 2019) [64-bit]
can’t open dataset stats.sub03+orig’

But the dataset is in the dir when I’m running the 3dbucket:

ls
3dDeconvolve.err mat.basewarp.aff12.1D
@epi_review.sub03 mat.r01.vr.aff12.1D
@ss_review_basic mat.r01.warp.aff12.1D
@ss_review_driver mat.r02.vr.aff12.1D
@ss_review_driver_commands mat.r02.warp.aff12.1D
S03_t1+orig.BRIK mat.r03.vr.aff12.1D
S03_t1+orig.HEAD mat.r03.warp.aff12.1D
S03_t1_al_junk+orig.BRIK mat.r04.vr.aff12.1D
S03_t1_al_junk+orig.HEAD mat.r04.warp.aff12.1D
S03_t1_al_junk_mat.aff12.1D motion_demean.1D
S03_t1_ns+orig.BRIK.gz motion_deriv.1D
S03_t1_ns+orig.HEAD motion_sub03_CENSORTR.txt
TSNR.sub03+orig.BRIK.gz motion_sub03_censor.1D
TSNR.sub03+orig.HEAD motion_sub03_enorm.1D
X.jpg out.allcostX.txt
X.nocensor.xmat.1D out.cormat_warn.txt
X.stim.xmat.1D out.gcor.1D
X.xmat.1D out.mask_ae_dice.txt
all_runs.sub03+orig.BRIK.gz out.mask_ae_overlap.txt
all_runs.sub03+orig.HEAD out.min_outlier.txt
anat_final.sub03+orig.BRIK.gz out.pre_ss_warn.txt
anat_final.sub03+orig.HEAD out.ss_review.sub03.txt
blur.epits.1D outcount.r01.1D
blur.errts.1D outcount.r02.1D
blur_est.sub03.1D outcount.r03.1D
censor_sub03_combined_2.1D outcount.r04.1D
corr_brain+orig.BRIK.gz outcount_rall.1D
corr_brain+orig.HEAD outcount_sub03_censor.1D
dfile.r01.1D pb00.sub03.r01.tcat+orig.BRIK
dfile.r02.1D pb00.sub03.r01.tcat+orig.HEAD
dfile.r03.1D pb00.sub03.r02.tcat+orig.BRIK
dfile.r04.1D pb00.sub03.r02.tcat+orig.HEAD
dfile_rall.1D pb00.sub03.r03.tcat+orig.BRIK
errts.sub03+orig.BRIK.gz pb00.sub03.r03.tcat+orig.HEAD
errts.sub03+orig.HEAD pb00.sub03.r04.tcat+orig.BRIK
files_ACF pb00.sub03.r04.tcat+orig.HEAD
final_epi_vr_base_min_outlier+orig.BRIK pb01.sub03.r01.despike+orig.BRIK
final_epi_vr_base_min_outlier+orig.HEAD pb01.sub03.r01.despike+orig.HEAD
fitts.sub03+orig.BRIK.gz pb01.sub03.r02.despike+orig.BRIK
fitts.sub03+orig.HEAD pb01.sub03.r02.despike+orig.HEAD
full_mask.sub03+orig.BRIK.gz pb01.sub03.r03.despike+orig.BRIK
full_mask.sub03+orig.HEAD pb01.sub03.r03.despike+orig.HEAD
gmean.errts.unit.1D pb01.sub03.r04.despike+orig.BRIK
ideal_01.1D pb01.sub03.r04.despike+orig.HEAD
ideal_02.1D pb02.sub03.r01.tshift+orig.BRIK
ideal_03.1D pb02.sub03.r01.tshift+orig.HEAD
ideal_04.1D pb02.sub03.r02.tshift+orig.BRIK
ideal_05.1D pb02.sub03.r02.tshift+orig.HEAD
ideal_06.1D pb02.sub03.r03.tshift+orig.BRIK
ideal_07.1D pb02.sub03.r03.tshift+orig.HEAD
ideal_08.1D pb02.sub03.r04.tshift+orig.BRIK
ideal_09.1D pb02.sub03.r04.tshift+orig.HEAD
ideal_10.1D pb03.sub03.r01.volreg+orig.BRIK
ideal_11.1D pb03.sub03.r01.volreg+orig.HEAD
ideal_12.1D pb03.sub03.r02.volreg+orig.BRIK
ideal_13.1D pb03.sub03.r02.volreg+orig.HEAD
ideal_14.1D pb03.sub03.r03.volreg+orig.BRIK
ideal_15.1D pb03.sub03.r03.volreg+orig.HEAD
ideal_16.1D pb03.sub03.r04.volreg+orig.BRIK
ideal_17.1D pb03.sub03.r04.volreg+orig.HEAD
ideal_18.1D pb04.sub03.r01.scale+orig.BRIK.gz
ideal_19.1D pb04.sub03.r01.scale+orig.HEAD
ideal_20.1D pb04.sub03.r02.scale+orig.BRIK.gz
ideal_21.1D pb04.sub03.r02.scale+orig.HEAD
ideal_22.1D pb04.sub03.r03.scale+orig.BRIK.gz
ideal_23.1D pb04.sub03.r03.scale+orig.HEAD
ideal_24.1D pb04.sub03.r04.scale+orig.BRIK.gz
ideal_25.1D pb04.sub03.r04.scale+orig.HEAD
ideal_filler.1D stats.REML_cmd
mask_anat.sub03+orig.BRIK.gz stats.sub03+orig.BRIK.gz
mask_anat.sub03+orig.HEAD stats.sub03+orig.HEAD
mask_epi_anat.sub03+orig.BRIK.gz stimuli
mask_epi_anat.sub03+orig.HEAD sum_ideal.1D
mask_epi_extents+orig.BRIK.gz vr_base_min_outlier+orig.BRIK
mask_epi_extents+orig.HEAD vr_base_min_outlier+orig.HEAD

I also tried to extract only one beta weight first:

3dbucket -prefix sub03_betas stats.sub03+orig’[1]’
3dbucket: No match.

Any suggestions would be really appreciated.

Thanks,
Joy

2

Hi, Joy-

For your second command, you would want to separate the numbers with commas, not spaces:


3dbucket -prefix sub03_betas stats.sub03+orig'[1,4,7,10,13,16,19,22,25,28,31,34,37,40,43,46,49,52,55,58,61,64,67,70,73]'

For the first one… I’m not sure; I just tried the following as a test on a dset to start at the [0]th volume and get every third one, through to the end, with:


3dbucket -prefix aaa FILE'[0..$(3)]'

and that worked for me.

–pt

3

I got this:
3dbucket -prefix sub03_betas stats.sub03+orig’[0…$(3)]’
Illegal variable name.

But this other command worked! Thank you very much!

Joy

4

Hi Joy,

It seems very likely that you are creating this command in an editor using “pretty” quotes of some sort, rather than the basic AFNI single quotes. That is why you are getting shell errors, because those quotes are not hiding the $ and ( from the shell.

Please copy-and-paste this command directly into your terminal, and see if it works:

3dbucket -prefix sub03_betas stats.sub03+orig'[0..$(3)]'
  • rick