ds002843-mriqc: "Can't use dataset with < 5 time points per voxel!"

[jbwexler]

Only for sub-dmp1095

Node: mriqc_wf.funcMRIQC.ComputeIQMs.outliers Working directory: /scratch1/03201/jbwexler/work_dir/mriqc/ds002843_sub-dmp1095/mriqc_wf/funcMRIQC/ComputeIQMs/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002843-mriqc..sourcedata..raw..sub-dmp1095..ses-scan1..func..sub-dmp1095_ses-scan1_task-risk_run-4_bold.nii.gz/outliers

Node inputs:

args = autoclip = False automask = False environ = {} fraction = True in_file = /scratch1/03201/jbwexler/work_dir/mriqc/ds002843_sub-dmp1095/mriqc_wf/funcMRIQC/fMRI_HMC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002843-mriqc..sourcedata..raw..sub-dmp1095..ses-scan1..func..sub-dmp1095_ses-scan1_task-risk_run-4_bold.nii.gz/motion_correct/sub-dmp1095_ses-scan1_task-risk_run-4_bold_valid_volreg.nii.gz interval = False legendre = False mask = /scratch1/03201/jbwexler/work_dir/mriqc/ds002843_sub-dmp1095/mriqc_wf/funcMRIQC/fMRIBrainMask/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002843-mriqc..sourcedata..raw..sub-dmp1095..ses-scan1..func..sub-dmp1095_ses-scan1_task-risk_run-4_bold.nii.gz/afni_msk/sub-dmp1095_ses-scan1_task-risk_run-4_bold_valid_volreg_tstat_mask.nii.gz out_file = outliers.out outliers_file = polort = qthr = 0.001 save_outliers = False

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/preprocess.py", line 1840, in _run_interface runtime = super(OutlierCount, 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: 3dToutcount -fraction -mask /scratch1/03201/jbwexler/work_dir/mriqc/ds002843_sub-dmp1095/mriqc_wf/funcMRIQC/fMRIBrainMask/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002843-mriqc..sourcedata..raw..sub-dmp1095..ses-scan1..func..sub-dmp1095_ses-scan1_task-risk_run-4_bold.nii.gz/afni_msk/sub-dmp1095_ses-scan1_task-risk_run-4_bold_valid_volreg_tstat_mask.nii.gz -qthr 0.00100 /scratch1/03201/jbwexler/work_dir/mriqc/ds002843_sub-dmp1095/mriqc_wf/funcMRIQC/fMRI_HMC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002843-mriqc..sourcedata..raw..sub-dmp1095..ses-scan1..func..sub-dmp1095_ses-scan1_task-risk_run-4_bold.nii.gz/motion_correct/sub-dmp1095_ses-scan1_task-risk_run-4_bold_valid_volreg.nii.gz Standard output:

Standard error: ++ 3dToutcount: AFNI version=AFNI_21.2.06 (Sep 1 2021) [64-bit] ESC[7m*+ WARNING:ESC[0m If you are performing spatial transformations on an oblique dset, such as /scratch1/03201/jbwexler/work_dir/mriqc/ds002843_sub-dmp1095/mriqc_wf/funcMRIQC/fMRIBrainMask/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002843-mriqc..sourcedata..raw..sub-dmp1095..ses-scan1..func..sub-dmp1095_ses-scan1_task-risk_run-4_bold.nii.gz/afni_msk/sub-dmp1095_ses-scan1_task-risk_run-4_bold_valid_volreg_tstat_mask.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/mriqc/ds002843_sub-dmp1095/mriqc_wf/funcMRIQC/fMRIBrainMask/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002843-mriqc..sourcedata..raw..sub-dmp1095..ses-scan1..func..sub-dmp1095_ses-scan1_task-risk_run-4_bold.nii.gz/afni_msk/sub-dmp1095_ses-scan1_task-risk_run-4_bold_valid_volreg_tstat_mask.nii.gz is 27.800009 degrees from plumb. ++ 53546 voxels in the mask ++ Oblique dataset:/scratch1/03201/jbwexler/work_dir/mriqc/ds002843_sub-dmp1095/mriqc_wf/funcMRIQC/fMRI_HMC/_infile..scratch1..03201..jbwexler..openneuro_derivatives..derivatives..mriqc..ds002843-mriqc..sourcedata..raw..sub-dmp1095..ses-scan1..func..sub-dmp1095_ses-scan1_task-risk_run-4_bold.nii.gz/motion_correct/sub-dmp1095_ses-scan1_task-risk_run-4_bold_valid_volreg.nii.gz is 27.800009 degrees from plumb. ** Can't use dataset with < 5 time points per voxel! Return code: 1

[effigies]

Clearly a prematurely terminated run.

$ nib-ls sub-dmp1095/ses-scan1/func/sub-dmp1095_ses-scan1_task-risk_run-*.nii.gz
sub-dmp1095/ses-scan1/func/sub-dmp1095_ses-scan1_task-risk_run-1_bold.nii.gz int16 [ 64,  64,  53, 104] 3.00x3.00x3.00x3.00   sform
sub-dmp1095/ses-scan1/func/sub-dmp1095_ses-scan1_task-risk_run-2_bold.nii.gz int16 [ 64,  64,  53, 104] 3.00x3.00x3.00x3.00   sform
sub-dmp1095/ses-scan1/func/sub-dmp1095_ses-scan1_task-risk_run-3_bold.nii.gz int16 [ 64,  64,  53, 104] 3.00x3.00x3.00x3.00   sform
sub-dmp1095/ses-scan1/func/sub-dmp1095_ses-scan1_task-risk_run-4_bold.nii.gz int16 [ 64,  64,  53,   4] 3.00x3.00x3.00x3.00   sform

We should probably just remove it before running fmriprep/mriqc.

[jbwexler]

Oh sorry forgot to mention this was an old version of MRIQC, v21.0.0rc2. Is it worth a rerun to see if this has been fixed?

[effigies]

I suspect nothing has changed. It's just a bad run, probably a subject who decided they couldn't take another full run. We should just drop it. I've created an issue for mriqc simply to ignore such short files.