ds000107: FATAL ERROR: 3dvolreg fails: base image has 0 nonzero voxels (< 100)

[jbwexler]

I got the following error for two (out of many) subjects when running mriqc on ds000107. I checked the original image sourcedata/raw/sub-18/func/sub-18_task-onebacktask_run-02_bold.nii.gz and surprisingly it seems load fine with nibabel and fsleyes. Though I couldn’t get it to load on openneuro with papaya.

Traceback (most recent call last): File "/opt/conda/bin/mriqc", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.8/site-packages/mriqc/cli/run.py", line 95, in main mriqc_wf.run(config.nipype.get_plugin()) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 164, in run self._clean_queue(jobid, graph, result=result) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/base.py", line 227, in _clean_queue raise RuntimeError("".join(result["traceback"])) RuntimeError: Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.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/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 sub-18_task-onebacktask_run-02_bold.1D -1Dmatrix_save sub-18_task-onebacktask_run-02_bold.aff12.1D -prefix sub-18_task-onebacktask_run-02_bold_volreg.nii.gz -zpad 4 -maxdisp1D sub-18_task-onebacktask_run-02_bold_md.1D /scratch1/03201/jbwexler/work_dir/mriqc/ds000107_sub-18/mriqc_wf/funcMRIQC/fMRI_HMC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds000107-mriqc..sourcedata..raw..sub-18..func..sub-18_task-onebacktask_run-02_bold.nii.gz/motion_correct/sub-18_task-onebacktask_run-02_bold.nii.gz Standard output: ​ Standard error: ++ 3dvolreg: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit] ++ Authored by: RW Cox ++ Coarse del was 10, replaced with 3 ++ WARNING: nifti_read_buffer(/scratch1/03201/jbwexler/work_dir/mriqc/ds000107_sub-18/mriqc_wf/funcMRIQC/fMRI_HMC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds000107-mriqc..sourcedata..raw..sub-18..func..sub-18_task-onebacktask_run-02_bold.nii.gz/motion_correct/sub-18_task-onebacktask_run-02_bold.nii.gz): data bytes needed = 286720 data bytes input = -1 number missing = 286721 (set to 0) NIFTI load bricks: cannot read brick 165 from '/scratch1/03201/jbwexler/work_dir/mriqc/ds000107_sub-18/mriqc_wf/funcMRIQC/fMRI_HMC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds000107-mriqc..sourcedata..raw..sub-18..func..sub-18_task-onebacktask_run-02_bold.nii.gz/motion_correct/sub-18_task-onebacktask_run-02_bold.nii.gz' FATAL ERROR: 3dvolreg fails: base image has 0 nonzero voxels (< 100) Program compile date = Sep 1 2021 Return code: 1

[jbwexler]

Got this error for two subs in ds002675-fmriprep

[jbwexler]

Also three subs in ds002306-fmriprep

[jbwexler]

@effigies

[effigies]

@jbwexler I'll need the traceback for fmriprep. It's not going to match the mriqc one.

[jbwexler]

Here's an example error log for ds002306:

Node: fmriprep_wf.single_subject_01_wf.func_preproc_task_training_run_12_wf.final_boldref_wf.gen_avg Working directory: /scratch1/03201/jbwexler/work_dir/fmriprep/ds002306_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_task_training_run_12_wf/final_boldref_wf/gen_avg

Node 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/multiproc.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_unwarped_merged_sliced.1D -1Dmatrix_save vol0000_unwarped_merged_sliced.aff12.1D -prefix vol0000_unwarped_merged_sliced_volreg.nii.gz -zpad 4 -maxdisp1D vol0000_unwarped_merged_sliced_md.1D /scratch1/03201/jbwexler/work_dir/fmriprep/ds002306_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_task_training_run_12_wf/final_boldref_wf/gen_avg/vol0000_unwarped_merged_sliced.nii.gz Standard output:

Standard error: ++ 3dvolreg: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit] ++ Authored by: RW Cox ESC[7m*+ WARNING:ESC[0m If you are performing spatial transformations on an oblique dset, such as /scratch1/03201/jbwexler/work_dir/fmriprep/ds002306_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_task_training_run_12_wf/final_boldref_wf/gen_avg/vol0000_unwarped_merged_sliced.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:/scratch1/03201/jbwexler/work_dir/fmriprep/ds002306_sub-01/fmriprep_wf/single_subject_01_wf/func_preproc_task_training_run_12_wf/final_boldref_wf/gen_avg/vol0000_unwarped_merged_sliced.nii.gz is 1.780153 degrees from plumb. ++ Coarse del was 10, replaced with 7 ESC[7m FATAL ERROR:ESC[0m 3dvolreg fails: base image has 0 nonzero voxels (< 100) Program compile date = Apr 6 2022 Return code: 1

[ruben-stanford]

I'm also having this issue when running fMRIPrep on some task data. Are there any updates for this?