search

nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
630 stars 292 forks source link

Exception raised while executing Node get_dummy #2917

Closed Heechberri closed 10 months ago

Heechberri commented 1 year ago

What happened?

For some of the subjects, fMRIprep outputs this error:

Node: fmriprep_22_0_wf.single_subject_EXCI0153_wf.func_preproc_ses_1_task_rest_wf.initial_boldref_wf.get_dummy Working directory: /tmp/work/fmriprep_22_0_wf/single_subject_EXCI0153_wf/func_preproc_ses_1_task_rest_wf/initial_boldref_wf/get_dummy

Node inputs:

in_file = /data/sub-EXCI0153/ses-1/func/sub-EXCI0153_ses-1_task-rest_bold.nii.gz n_volumes = 40 nonnegative = True zero_dummy_masked = 20

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command raise NodeExecutionError( nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node get_dummy.

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.9/site-packages/niworkflows/interfaces/bold.py", line 84, in _run_interface data = img.get_fdata(dtype="float32")[..., :self.inputs.n_volumes] File "/opt/conda/lib/python3.9/site-packages/nibabel/dataobj_images.py", line 355, in get_fdata data = np.asanyarray(self._dataobj, dtype=dtype) File "/opt/conda/lib/python3.9/site-packages/nibabel/arrayproxy.py", line 370, in array arr = self._get_scaled(dtype=dtype, slicer=()) File "/opt/conda/lib/python3.9/site-packages/nibabel/arrayproxy.py", line 337, in _get_scaled scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter) File "/opt/conda/lib/python3.9/site-packages/nibabel/arrayproxy.py", line 311, in _get_unscaled return array_from_file(self._shape, File "/opt/conda/lib/python3.9/site-packages/nibabel/volumeutils.py", line 468, in array_from_file raise IOError(f"Expected {n_bytes} bytes, got {n_read} bytes from " OSError: Expected 182241280 bytes, got 35153493 bytes from object

What command did you use?

I used the code below, and for majority of the subjects fMRIprep ran smoothly

#version 22.0.0
sudo docker run -ti \
-v $disk/$project_dir/$bids_dir:/data:ro \
-v $disk/$project_dir/$preprocessed_dir:/fMRI \
-v $freesurfer_licence:/opt/freesurfer/license.txt \
-v $plugin_file:/plugin.yml \
nipreps/fmriprep:22.0.0 \
/data /fMRI participant \
--error-on-aroma-warnings --use-aroma \
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin6Asym:res-1 MNI152NLin2009cAsym:res-2 MNI152NLin2009cAsym:res-1 \
--fd-spike-threshold 0.5 \
--dvars-spike-threshold 20 \
--use-plugin /plugin.yml \
--dummy-scans 5 \
--write-graph \
--n_cpus '16' \
--omp-nthreads 4 \
--mem 40GB \
--verbose \
--resource-monitor

What version of fMRIPrep are you running?

22.0.0

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Node: fmriprep_22_0_wf.single_subject_EXCI0153_wf.func_preproc_ses_1_task_rest_wf.initial_boldref_wf.get_dummy
Working directory: /tmp/work/fmriprep_22_0_wf/single_subject_EXCI0153_wf/func_preproc_ses_1_task_rest_wf/initial_boldref_wf/get_dummy

Node inputs:

in_file = /data/sub-EXCI0153/ses-1/func/sub-EXCI0153_ses-1_task-rest_bold.nii.gz
n_volumes = 40
nonnegative = True
zero_dummy_masked = 20

Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node get_dummy.

Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.9/site-packages/niworkflows/interfaces/bold.py", line 84, in _run_interface
data = img.get_fdata(dtype="float32")[..., :self.inputs.n_volumes]
File "/opt/conda/lib/python3.9/site-packages/nibabel/dataobj_images.py", line 355, in get_fdata
data = np.asanyarray(self._dataobj, dtype=dtype)
File "/opt/conda/lib/python3.9/site-packages/nibabel/arrayproxy.py", line 370, in array
arr = self._get_scaled(dtype=dtype, slicer=())
File "/opt/conda/lib/python3.9/site-packages/nibabel/arrayproxy.py", line 337, in _get_scaled
scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
File "/opt/conda/lib/python3.9/site-packages/nibabel/arrayproxy.py", line 311, in _get_unscaled
return array_from_file(self._shape,
File "/opt/conda/lib/python3.9/site-packages/nibabel/volumeutils.py", line 468, in array_from_file
raise IOError(f"Expected {n_bytes} bytes, got {n_read} bytes from "
OSError: Expected 182241280 bytes, got 35153493 bytes from object

    could the file be damaged?

Additional information / screenshots

No response

effigies commented 1 year ago

It looks like the file is damaged. Have you inspected /data/sub-EXCI0153/ses-1/func/sub-EXCI0153_ses-1_task-rest_bold.nii.gz with a third-party tool? My guess is if you try to look at the last volume, you'll get an error in the other tool. This can happen if a file failed to be fully copied. Re-copying it from its source (or re-converting it, if the source is DICOM) should resolve it.

Heechberri commented 1 year ago

Hi effigies :)

Thanks for the quick reply.

I did inspect the file in both MRIcron and fsleyes, and they didn't appear to be different than the other files. Could I send you the file if you don't mind?

I wil try exporting them from the scanner and converting them again as well :)

effigies commented 1 year ago

If you can run fsleyes, you should also be able to run:

python -c "import nibabel as nb; nb.load('/data/sub-EXCI0153/ses-1/func/sub-EXCI0153_ses-1_task-rest_bold.nii.gz').get_fdata()"

I would expect this to have the same failure case as get_dummy(). If that succeeds, I would try re-running, as there may have been some one-off hiccup.