Question about program 3dDeconvolve

Hello all member!

I ran 3dDeconvolve with the arguments listed in the script below and saved the bucket to a NIfTI file. When I view the verbose header information for the file containing the bucket output, I can confirm that the file contains all of the expected sub-bricks with beta weights for each regressor specified in 3dDeconvolve. However, when I view the bucket output in a program like FSLview, only one volume is present.


3dDeconvolve -input \
…/epi_run1_fnirt_6run_melodic.ica/denoised_data.nii.gz \
…/epi_run2_fnirt_6run_melodic.ica/denoised_data.nii.gz \
…/epi_run3_fnirt_6run_melodic.ica/denoised_data.nii.gz \
…/epi_run4_fnirt_6run_melodic.ica/denoised_data.nii.gz \
…/epi_run5_fnirt_6run_melodic.ica/denoised_data.nii.gz \
…/epi_run6_fnirt_6run_melodic.ica/denoised_data.nii.gz \
-jobs 4 \
-polort 2 -num_stimts 4 \
-local_times \
-stim_times_IM 1 /deep/heller/work/savorema/1DDirs/${i}_1Dfiles/AFNI_win_local_times.txt ‘SPMG3’ \
-stim_label 1 Win \
-local_times \
-stim_times 2 /deep/heller/work/savorema/1DDirs/${i}_1Dfiles/AFNI_loss_local_times.txt ‘SPMG3’ \
-stim_label 2 Loss \
-stim_file 3 /deep/heller/work/savorema/anatDirs/${i}_anat/WM_all.txt \
-stim_label 3 WM_mask \
-stim_file 4 /deep/heller/work/savorema/anatDirs/${i}_anat/CSF_all.txt \
-stim_label 4 CSF_mask \
-xsave -xjpeg /deep/heller/work/savorema/${i}/FinancialWin/win_glm/win_glm \
-errts /deep/heller/work/savorema/${i}/FinancialWin/win_glm/residuals_win_IM.nii \
-bout \
-bucket /deep/heller/work/savorema/${i}/FinancialWin/win_glm/win_glm.nii

Is there any way to write each sub-brick from this bucket dataset onto the time dimension of a 4D dataset? To clarify, this would mean that each sub-brick would be represented in a 3D volume of a 4D dataset. I have searched the internet for information but still have no reasonable answer.

I am hoping to index through sub-bricks of the bucket dataset to perform a beta series correlation analysis, and it will be easier to carry out this analysis in matlab if all sub-bricks are listed along the 4th dimension of a single dataset.

Thanks in advance!

NIFTI datasets that have multiple types of volumes as
are output by 3dDeconvolve are actually beyond the
NIFTI standard, and most packages will not understand

Consider using 3dTsplit4D to break that into individual
volumes for viewing in FSL. I don’t know how it would
handle a collection of betas or t-stats.

  • rick