ds001621-mriqc: ValueError: Cannot apply_along_axis when any iteration dimensions are 0

[jbwexler]

For about half the subjects in ds001621 I got either the above error or the following one: Can't use dataset with < 5 time points per voxel!

I'm posting the full error output of both here:

MELODIC outputs not found, assuming it didn't converge. 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 158, in main mriqc_wf.run(**_plugin) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 632, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 184, in run self._clean_queue(jobid, graph, result=result) File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 256, in _clean_queue raise RuntimeError("".join(result["traceback"])) RuntimeError: Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 60, 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._runinterface(execute=True) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in run_interface return self._runcommand(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 419, in ru n runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/algorithms/confounds.py", line 166, in _r un_interface dvars = compute_dvars( File "/opt/conda/lib/python3.8/site-packages/nipype/algorithms/confounds.py", line 1057, in c ompute_dvars ar1 = np.apply_along_axis( File "<__array_function__ internals>", line 180, in apply_along_axis File "/opt/conda/lib/python3.8/site-packages/numpy/lib/shape_base.py", line 376, in apply_alo ng_axis raise ValueError( ValueError: Cannot apply_along_axis when any iteration dimensions are 0

The other error:

MELODIC outputs not found, assuming it didn't converge. 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 158, in main mriqc_wf.run(**_plugin) File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/workflows.py", line 632, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 184, in run self._clean_queue(jobid, graph, result=result) File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 256, in _clean_que ue raise RuntimeError("".join(result["traceback"])) RuntimeError: Traceback (most recent call last): File "/opt/conda/lib/python3.8/site-packages/mriqc/engine/plugin.py", line 60, 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._runcommand(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 419, in ru n runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/afni/preprocess.py", line 1845 , in _run_interface runtime = super(OutlierCount, self)._run_interface( File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 814, in _r un_interface self.raise_exception(runtime) File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 741, in ra ise_exception raise RuntimeError( RuntimeError: Command: 3dToutcount -fraction -mask /scratch1/03201/jbwexler/work_dir/mriqc/ds001621_sub-02/mriqc_wf/fu ncMRIQC/fMRIBrainMask/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives. .mriqc..ds001621-mriqc..sourcedata..raw..sub-02..func..sub-02_task-commstruc_run-01_bold.nii.gz /afni_msk/sub-02_task-commstruc_run-01_bold_volreg_tstat_mask.nii.gz -qthr 0.00100 /scratch1/03 201/jbwexler/work_dir/mriqc/ds001621_sub-02/mriqc_wf/funcMRIQC/fMRI_HMC/_infile..scratch1..03 201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds001621-mriqc..sourcedata..raw..sub- 02..func..sub-02_task-commstruc_run-01_bold.nii.gz/motion_correct/sub-02_task-commstrucrun-01 bold_volreg.nii.gz Standard output:

Standard error: ++ 3dToutcount: AFNI version=AFNI_22.0.17 (Mar 10 2022) [64-bit] ++ 34406 voxels in the mask ** Can't use dataset with < 5 time points per voxel! Return code: 1