3dBucket error: output dataset name 'filename" conflicts with existing file

AFNI Message Board
1

Hello,

new user here and struggling with what probably is a basic error.

Running the preprocessing I get this error and have searched online and on the message board to figure out what it could be to no avail.

The error is:

#Script is running (command trimmed):
3dNotes -h “auto_warp.py -base HaskinsPeds_NL_template1.0+tlrc -input
sub-006_ses-T1_T1w_ns+orig -skull_strip_input no”
./sub-006_ses-T1_T1w_ns.aw.nii

3dbucket -prefix sub-006_ses-T1_T1w_ns awpy/sub-006_ses-T1_T1w_ns.aw.nii
++ 3dbucket: AFNI version=AFNI_19.0.06 (Feb 4 2019) [64-bit]
** ERROR: output dataset name ‘sub-006_ses-T1_T1w_ns’ conflicts with existing file
** ERROR: dataset NOT written to disk!

For context, I am adding the afni_proc.py in case it’s an error stemming from some specs in previous stages.

set datapath = /Users/nens.lab/Documents/PEN802_Spring2019/Scans/sub-006

afni_proc.py -subj_id prova2                                                             \
          -blocks tshift align tlrc volreg blur mask scale 	                          \
          regress 											  \
          -copy_anat $datapath/ses-T1/anat/sub-006_ses-T1_T1w.nii.gz \
          -dsets                                                                                           \
              $datapath/ses-T1/func/sub-006_ses-T1_task-Sub_run-0?_bold.nii.gz \
          -align_opts_aea -cost lpc+ZZ                                                      \
          -tshift_interp -quintic   						                   \
          -tlrc_base HaskinsPeds_NL_template1.0+tlrc                             \
          -tlrc_NL_warp                                                                              \
          -volreg_align_to MIN_OUTLIER                                                  \
          -volreg_align_e2a                                                                        \
          -volreg_tlrc_warp                                                                         \
          -regress_motion_per_run                                                            \
          -regress_censor_motion 0.3                                                       \
          -regress_censor_outliers 0.1						          \
          -regress_reml_exec 				                                          \
          -regress_stim_times                                                                    \
              $datapath/ses-T1/stim/ETrue.tsv                                            \
              $datapath/ses-T1/stim/HTrue.tsv                                            \
              $datapath/ses-T1/stim/EFalse.tsv                                           \
              $datapath/ses-T1/stim/HFalse.tsv                                           \
              $datapath/ses-T1/stim/control_s.tsv		                           \
          -regress_stim_labels                                                                    \
              ET HT EF HF Ctrl_s                                                                 \
          -regress_basis GAM                                        		                   \
          -regress_opts_3dD                                                                      \
              -jobs 4                                                                                     \
              -gltsym 'SYM: HTrue - ETrue' -glt_label 1 Ht-Et                      \
              -gltsym 'SYM: HFalse - EFalse' -glt_label 2 Hf-Ef                   \
          -regress_est_blur_epits							          \
          -regress_est_blur_errts                                                               \

Thank you for any help or hint leading to the solution!
Ilaria

2

Hi Ilaria,

What is the output from:

3dinfo -av_space -space $datapath/ses-T1/anat/sub-006_ses-T1_T1w.nii.gz

I expect that it will say “+tlrc”, in which case you may need to set

AFNI_NIFTI_VIEW = orig

either in the shell scripts or in your .afnirc file.

  • rick
3

Dear Rick,

my .afnirc already contains the AFNI_NIFTI_VIEW = orig
I have added: setenv AFNI_NIFTI_VIEW orig to the proc. file at the very top… but the same error was returned.

Should I use 3dcopy to convert my nii file into BRIK & HEAD and make sure they are +orig?

thank you

Ilaria

UPDATE:
I have also converted my anat and func files with 3dcopy for the subject and the same message returned. I thought this would have resolved the issue if it was a file type problem. I guess it might be in the blocks or specs I have selected?
this it a copy of the proc file

afni_proc.py -subj_id provaOrig
-blocks tshift align tlrc volreg blur mask scale regress
-copy_anat /Users/nens.lab/Documents/PEN802_Spring2019/Scans/sub-006/ses-T1/anat/sub-006_ses-T1_T1w+orig.BRIK
-dsets /Users/nens.lab/Documents/PEN802_Spring2019/Scans/sub-006/ses-T1/func/sub-006_ses-T1_task-Sub_run-01_bold+orig.BRIK
/Users/nens.lab/Documents/PEN802_Spring2019/Scans/sub-006/ses-T1/func/sub-006_ses-T1_task-Sub_run-02_bold+orig.BRIK
-align_opts_aea
-cost lpc+ZZ
-tshift_interp -quintic
-tlrc_base HaskinsPeds_NL_template1.0+tlrc
-tlrc_NL_warp
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a
-volreg_tlrc_warp
-regress_motion_per_run
-regress_censor_motion 0.3
-regress_censor_outliers 0.1
-regress_reml_exec
-regress_stim_times /Users/nens.lab/Documents/PEN802_Spring2019/Scans/sub-006/ses-T1/stim/ETrue.tsv
/Users/nens.lab/Documents/PEN802_Spring2019/Scans/sub-006/ses-T1/stim/HTrue.tsv
/Users/nens.lab/Documents/PEN802_Spring2019/Scans/sub-006/ses-T1/stim/EFalse.tsv
/Users/nens.lab/Documents/PEN802_Spring2019/Scans/sub-006/ses-T1/stim/HFalse.tsv
/Users/nens.lab/Documents/PEN802_Spring2019/Scans/sub-006/ses-T1/stim/control_s.tsv
-regress_stim_labels ET HT EF HF Ctrl_s
-regress_basis GAM
-regress_opts_3dD
-jobs 4
-gltsym SYM: HTrue - ETrue -glt_label 1 Ht-Et
-gltsym SYM: HFalse - EFalse -glt_label 2 Hf-Ef
-regress_est_blur_epits
-regress_est_blur_errts

your help is greatly appreciated!
Ilaria

4

Hi Ilaria,

If you would not mind, please send me the actual proc.* script and corresponding output.proc.* text output file from running it (in this second case with the AFNI dataset input). That would be helpful in understanding what is going wrong.

Thanks,

  • rick