mri_read_ascii error when opening @file for 3dTshift -tpattern

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1

AFNI gurujis–

My goal is use the -tpattern @filename option within afni_proc to do slice-time correction using the slice timings provided in a BIDS .json file. I’ve managed to confound my efforts in two easy steps:

First, read slicenums lines from a BIDS format .json file to get the slice-timing for the EPI data. Dump it into the 1D file slicetimes.1D

    # first set a variable indicating the number of slices
    set slicenums="`3dinfo -nk rest.nii`"
    # next, read slicenums of slice-timing info from the .json
    set slicetimes = "`less rest.json | grep -A ${slicenums} SliceTiming | grep -Eo '[0-9.]{1,}'`"
    echo ${slicetimes} > slicetimes.1D

Second, call up afni_proc and, among several other things, ask it to read the slice-timing from slicetimes.1D

    afni_proc.py -subj_id ${subID} \
    -dsets rest.nii \
    -copy_anat T1.nii \
    -blocks despike tshift align tlrc volreg mask regress \
    -tshift_opts_ts -tpattern @slicetimes.1D \
    -mask_segment_anat yes \
    -mask_segment_erode yes \
    -align_opts_aea -ginormous_move -deoblique on -cost lpc+ZZ \
    -tcat_remove_first_trs 4 \
    -tlrc_NL_warp \
    -tlrc_base MNI152_2009_template.nii.gz \
    -volreg_align_to MIN_OUTLIER \
    -volreg_tlrc_warp \
    -volreg_warp_dxyz 3.0 \
    -regress_motion_per_run \
    -regress_censor_motion 0.3 \
    -regress_censor_outliers 0.1 \
    -regress_apply_mot_types demean deriv \
    -regress_compute_tsnr yes \
    -regress_anaticor_fast \
    -regress_bandpass 0.001 0.198 \
    -execute

The following error results:
** ERROR: mri_read_ascii: couldn’t open file slicetimes.1D
** FATAL ERROR: Can’t read tpattern file slicetimes.1D

The file is, indeed, readable in other contexts, though. I can 1dplot it and if I use 3dTshift the old-fashioned way, it works fine:
3dTshift -prefix foo -tpattern @slicetimes.1D rest.nii

Something with how the afni_proc wrapper wants to read the file, perhaps? Sorry. Hope I’m not doing something ridiculous but I’m at the bottom of my debug stack…

Oh, and: Precompiled binary linux_ubuntu_16_64: Jun 18 2019 (Version AFNI_19.1.21 ‘Caligula’)

Thanks!

2

Try specifying the full path to the slicetimes.1D file.

You can try to use -copy_files inside the afni_proc.py script setup to copy the necessary slicetimes file like the anatomical is copied. My memory is that this also works.

3

Thanks, Peter. It’s after work hours here in Sweden but I’ll try tomorrow and report back.

4

Follow-up: Both options work nicely. Thanks!