I’m encountering the following error message that causing terrible co-registration to my data:
Inputs:
in_file:
mc_method: AFNI
nonnegative: True
t_mask:
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/images.py", line 322, in _run_interface
res = Volreg(
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/afni/base.py", line 124, in _run_interface
return super(AFNICommandBase, self)._run_interface(
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 822, in _run_interface
self.raise_exception(runtime)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 749, in raise_exception
raise RuntimeError(
RuntimeError: Command:
3dvolreg -Fourier -twopass -1Dfile vol0000_xform-00000_clipped_merged_sliced.1D -1Dmatrix_save vol0000_xform-00000_clipped_merged_sliced.aff12.1D -prefix vol0000_xform-00000_clipped_merged_sliced_volreg.nii.gz -zpad 4 -maxdisp1D vol0000_xform-00000_clipped_merged_sliced_md.1D /N/scratch/dlevitas/fmriprep-21.0.2_temp/sub-41/fmriprep_wf/single_subject_41_wf/func_preproc_task_pacpal_run_2_wf/bold_t1_trans_wf/bold_reference_wf/gen_avg/vol0000_xform-00000_clipped_merged_sliced.nii
Standard output:
Standard error:
++ 3dvolreg: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: RW Cox
** AFNI converts NIFTI_datatype=4 (INT16) in file /N/scratch/dlevitas/fmriprep-21.0.2_temp/sub-41/fmriprep_wf/single_subject_41_wf/func_preproc_task_pacpal_run_2_wf/bold_t1_trans_wf/bold_reference_wf/gen_avg/vol0000_xform-00000_clipped_merged_sliced.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Coarse del was 10, replaced with 5
Fatal Signal 11 (SIGSEGV) received
fft_shift2
apply_zshear
apply_3shear
THD_rota_vol
mri_3dalign_one
3dvolreg main
Bottom of Debug Stack
** Command line was:
3dvolreg -Fourier -twopass -1Dfile vol0000_xform-00000_clipped_merged_sliced.1D -1Dmatrix_save vol0000_xform-00000_clipped_merged_sliced.aff12.1D -prefix vol0000_xform-00000_clipped_merged_sliced_volreg.nii.gz -zpad 4 -maxdisp1D vol0000_xform-00000_clipped_merged_sliced_md.1D /N/scratch/dlevitas/fmriprep-21.0.2_temp/sub-41/fmriprep_wf/single_subject_41_wf/func_preproc_task_pacpal_run_2_wf/bold_t1_trans_wf/bold_reference_wf/gen_avg/vol0000_xform-00000_clipped_merged_sliced.nii
** AFNI version = AFNI_22.1.02 Compile date = Apr 6 2022
** [[Precompiled binary linux_openmp_64: Apr 6 2022]]
** Program Death **
** 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 /N/u/dlevitas/Carbonate/.afni.crashlog
Return code: 1
I’ve tried re-running fmriprep (version 21.0.2) a few times with new freesurfer and working directories, but the issue persists. I tried looking into the working directory files to see where this first occurs, and it appears to be during the unwarp_wf/resample workflow, where the unwarped volumes are severely cut (and in some cases appear reoriented). This issue only occurs for a single subject in my dataset, but nothing about the BIDS data seems out of the ordinary for this subject. I haven’t found any solutions online and wanted to see if anyone here might know what the issue is? For reference, my fmriprep command was:
unset PYTHONPATH; singularity run \
-B ${bids_root_dir}:${bids_root_dir} \
-B /N/dcwan/projects/irf/templateflow:/opt/templateflow
-B ${work_dir}:${work_dir} \
-B ${output_dir}:${output_dir} \
/N/dcwan/projects/irf/containers/fmriprep-${fmriprep_version}.simg \
$bids_root_dir $output_dir \
participant \
--participant-label $s \
--skip-bids-validation \
--md-only-boilerplate \
--fs-license-file $FREESURFER_HOME/license.txt \
--fs-subjects-dir $output_dir/sourcedata/freesurfer/sub-${s} \
--output-spaces MNI152NLin6Asym:res-2 \
--nthreads $cores \
--stop-on-first-crash \
--resource-monitor \
--low-mem \
--mem_mb $reduced_mem \
--use-plugin $bids_root_dir/fmriprep_plugin_${s}.yml \
--use-aroma \
--aroma-melodic-dimensionality 100 \
--dummy-scans $dummy_scans \
--verbose \
--bids-filter-file ${bids_root_dir}/code/bids_filter_file.json \
--output-layout bids \
-w $work_dir/sub-${s}
Thanks,
Dan