ireps specified but no corresponding result file shown in the folder

AFNI Message Board
1

Hello,

I am doing HRF deconvolution using afni_proc.py, the process finished without error but I could not find the output specified by -ireps in the result folder. Could you please help me tackle this issue? Here is the afni_proc.py code

afni_proc.py -subj_id sub-ep0583s2
-out_dir /mnt/e/EP_EEGfMRI_deconvolution/sub-ep0583s2/Rsw_CSPLIN
-blocks despike tshift align volreg mask blur
scale regress
-dsets /mnt/e/EP_EEGfMRI_deconvolution/sub-ep0583s2/func/sub-ep0583s2_task-spike_run-1_bold.nii.gz
/mnt/e/EP_EEGfMRI_deconvolution/sub-ep0583s2/func/sub-ep0583s2_task-spike_run-2_bold.nii.gz
/mnt/e/EP_EEGfMRI_deconvolution/sub-ep0583s2/func/sub-ep0583s2_task-spike_run-3_bold.nii.gz
-tcat_remove_first_trs 6
-radial_correlate_blocks tcat volreg
-copy_anat /mnt/e/EP_EEGfMRI_deconvolution/derivatives/afni/sub-ep0583s2/anat/anatSS.sub-ep0583s2.nii
-anat_has_skull no
-anat_follower anat_w_skull anat /mnt/e/EP_EEGfMRI_deconvolution/sub-ep0583s2/anat/sub-ep0583s2_T1w.nii.gz
-volreg_align_to MIN_OUTLIER
-volreg_align_e2a
-volreg_warp_dxyz 3.5
-align_opts_aea -check_flip -cost lpc+ZZ -giant_move -AddEdge
-align_unifize_epi local
-mask_epi_anat yes
-blur_in_mask yes
-blur_size 6.5
-blur_to_fwhm
-regress_stim_times /mnt/e/EP_EEGfMRI_deconvolution/derivatives/afni/sub-ep0583s2/events/sub-ep0583s2_spike_Rsw_events.1D
-regress_stim_labels Rsw
-regress_stim_times_offset -11.4
-regress_basis ‘CSPLIN(-3.8,20.9,14)’
-regress_stim_types times
-regress_local_times
-regress_motion_per_run
-regress_censor_motion 0.3
-regress_censor_outliers 0.05
-regress_compute_fitts
-regress_make_ideal_sum sum_ideal.1D
-regress_est_blur_epits
-regress_est_blur_errts
-regress_run_clustsim yes
-regress_reml_exec
-regress_opts_reml -GOFORIT 99
-regress_opts_3dD
-bout
-jobs 16
-allzero_OK
-GOFORIT 99
-regress_3dD_stop
-html_review_style pythonic

And here is the 3dDconvole section in the whole AFNI process coded generated by afni_proc.py. There is a line -iresp 1 iresp_Rsw.$subj. Please also find the whole process file here https://drive.google.com/file/d/1vyyvAT5oyecGm8nY61FD2cd26H9Sck2G/view?usp=sharing

3dDeconvolve -input pb05.$subj.r*.scale+orig.HEAD
-censor censor_${subj}_combined_2.1D
-ortvec mot_demean.r01.1D mot_demean_r01
-ortvec mot_demean.r02.1D mot_demean_r02
-ortvec mot_demean.r03.1D mot_demean_r03
-polort 3
-local_times
-num_stimts 1
-stim_times 1 stimuli/offset_sub-ep0583s2_spike_Rsw_events.1D
‘CSPLIN(-3.8,20.9,14)’
-stim_label 1 Rsw
-iresp 1 iresp_Rsw.$subj
-bout
-jobs 16
-allzero_OK
-GOFORIT 99
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg
-x1D_uncensored X.nocensor.xmat.1D
-errts errts.${subj}
-x1D_stop
-bucket stats.$subj

Thanks,
Zhengchen

2

Hi Zhengchen,

There should be a dataset with a name starting with iresp_Rsw. If you would like, please send direct email (click on my name) with the text output from running 3dDeconvolve, or maybe just the output.proc.SUBJECT file.

  • rick
3

Hi Rick,

Thank you very much. I’ve sent you the email.

Zhengchen

4

Oh, thanks for the output. I did not notice, but your commands include -regress_reml_exec and -regress_3dD_stop, so 3dDeconvolve is not being used to perform the regression. And unfortunately, 3dREMLfit is not able to create iresp output, that only works in 3dDeconvolve which is not being used.

You can use 3dbucket or 3dTcat to extract the betas of interest from the 3dREMLfit output. It is slightly inconvenient, but easy to do.

  • rick