full disk + can't load data set + cant open input dataset ERRORS with afni_proc.py

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1

Hi,

I've been using this code for preprocessing of 3 participants so far and haven't had an issue:
afni_proc.py -subj_id 8345_6 -script proc.8495_6subj -scr_overwrite -blocks tshift align tlrc volreg blur mask scale regress -dsets Oddball?_8345.nii -copy_anat anatSS.sub-8345.nii -volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -blur_size 4.0 -tlrc_base MNI152_2009_template.nii.gz -tlrc_NL_warp -tlrc_NL_warped_dsets anatQQ.sub-8345.nii anatQQ.sub-8345.aff12.1D anatQQ.sub-8345_WARP.nii -anat_has_skull no -regress_stim_times Stand_Regress_Correct_Onset_NEU_8345.txt Stand_Regress_Correct_Onset_NEG_8345.txt Odd_Regress_Correct_Onset_NEU_8345.txt Odd_Regress_Correct_Onset_NEG_8345.txt -regress_stim_labels StandardNeuC StandardNegC OddballNeuC OddballNegC -regress_basis 'BLOCK(2,1)' -regress_opts_3dD -gltsym 'SYM: OddballNeuC -StandardNeuC' -glt_label 1 OddNeu-StandNeu -gltsym 'SYM: OddballNegC -StandardNegC' -glt_label 2 OddNeg-StandNeg -regress_motion_per_run -regress_censor_motion 0.3 -regress_censor_outliers 0.05 -regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits -regress_est_blur_errts -execute

but now I just got this error:
*+ WARNING: 3dTproject input data :: 250473 vectors are constant *+ WARNING: Disk space: writing file ./det.d01+tlrc.BRIK (6168 MB), but only 4088 free MB on disk gzip: stdout: No space left on device Fatal Signal 13 (SIGPIPE) received THD_write_3dim_dataset 3dTproject Bottom of Debug Stack ** AFNI version = AFNI_25.1.07 Compile date = May 1 2025 ** [[Precompiled binary linux_ubuntu_16_64: May 1 2025]] ** Program Death ** tee: output.proc.8495_6subj: No space left on device ** If you report this crash to the AFNI message board, ** please copy the error messages EXACTLY, and give ** the command line you used to run the program, and ** any other information needed to repeat the problem. ** You may later be asked to upload data to help debug. ** Crash log is appended to file /home/jshelp/.afni.crashlog -- radcor: running correlation on dataset all_runs.8345_6+tlrc.HEAD ... ++ 3dcalc: AFNI version=AFNI_25.1.07 (May 1 2025) [64-bit] ++ Authored by: A cast of thousands gzip: ./det.d01+tlrc.BRIK.gz: unexpected end of file *** failure while reading from brick file ./det.d01+tlrc.BRIK *** desired 6467641344 bytes but only got 6004034831 *** Unix error message: No such file or directory THD_load_datablock 3dcalc main ** FATAL ERROR: Can't load dataset './det.d01+tlrc.BRIK': is it complete? ** Program compile date = May 1 2025 ++ radcor: merge blur: rad 20, FWHM 40 ++ 3dmerge: AFNI version=AFNI_25.1.07 (May 1 2025) [64-bit] *** cannot open dataset rm.emasked.d01+tlrc Program 3dmerge 3dmerge: edit and combine 3D datasets, by RW Cox ++ 3dTcorrelate: AFNI version=AFNI_25.1.07 (May 1 2025) [64-bit] ** FATAL ERROR: Can't open input dataset sphere.mean.20.d01+tlrc ** Program compile date = May 1 2025 ** missing correlation result radcor.20.d01.all_runs.corr+tlrc.HEAD

AFNI version info (afni -ver): AFNI_25.1.03

Any help is appreciated! Thanks!

2

Hi-

The fatal part of that warning is:

WARNING: Disk space: writing file ./det.d01+tlrc.BRIK (6168 MB), but only 4088 free MB on disk gzip: stdout: No space left on device

So, it appears you are out of disk space on that computer, and will have to free some up before you can create new files.

Also, just note, I made a vertically aligned version of your AP command, which is easier to read, in case that is useful:

afni_proc.py                                                                 \
    -subj_id                  8345_6                                         \
    -script                   proc.8495_6subj                                \
    -scr_overwrite                                                           \
    -blocks                   tshift align tlrc volreg blur mask scale       \
                              regress                                        \
    -dsets                    Oddball?_8345.nii                              \
    -copy_anat                anatSS.sub-8345.nii                            \
    -volreg_align_to          MIN_OUTLIER                                    \
    -volreg_align_e2a                                                        \
    -volreg_tlrc_warp                                                        \
    -blur_size                4.0                                            \
    -tlrc_base                MNI152_2009_template.nii.gz                    \
    -tlrc_NL_warp                                                            \
    -tlrc_NL_warped_dsets     anatQQ.sub-8345.nii anatQQ.sub-8345.aff12.1D   \
                              anatQQ.sub-8345_WARP.nii                       \
    -anat_has_skull           no                                             \
    -regress_stim_times       Stand_Regress_Correct_Onset_NEU_8345.txt       \
                              Stand_Regress_Correct_Onset_NEG_8345.txt       \
                              Odd_Regress_Correct_Onset_NEU_8345.txt         \
                              Odd_Regress_Correct_Onset_NEG_8345.txt         \
    -regress_stim_labels      StandardNeuC StandardNegC OddballNeuC          \
                              OddballNegC                                    \
    -regress_basis            'BLOCK(2,1)'                                   \
    -regress_opts_3dD         -gltsym 'SYM: OddballNeuC -StandardNeuC'       \
                              -glt_label 1 OddNeu-StandNeu                   \
                              -gltsym 'SYM: OddballNegC -StandardNegC'       \
                              -glt_label 2 OddNeg-StandNeg                   \
    -regress_motion_per_run                                                  \
    -regress_censor_motion    0.3                                            \
    -regress_censor_outliers  0.05                                           \
    -regress_make_ideal_sum   sum_ideal.1D                                   \
    -regress_est_blur_epits                                                  \
    -regress_est_blur_errts                                                  \
    -execute

And as some additional processing considerations, I note the following comments, with some extra descriptions of options available here:

  • Reynolds RC, Glen DR, Chen G, Saad ZS, Cox RW, Taylor PA (2024). Processing, evaluating and understanding FMRI data with afni_proc.py. Imaging Neuroscience 2:1-52.
    https://doi.org/10.1162/imag_a_00347

For some extra QC, you might want to add:

-volreg_compute_tsnr      yes

as well as:

-radial_correlate_blocks  tcat volreg regress

For improved EPI-anatomical alignment (of human FMRI data), I would add:

-align_unifize_epi        local
-align_opts_aea           -giant_move -cost lpc+ZZ -check_flip

For an improved mask, I would add:

-mask_epi_anat            yes

--pt

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