dwi crash report - expected file size not reached
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Cassandra Marotta
May 16, 2024, 8:19:30 PM5/16/24
to mriqc-users
Hello
I am trying to analyse dwi data with version 24.0.0 but I am encountering an error.
I am running this inside a singularity container on a HPC cluster with 1 P4 GPU, 6 CPUs and 55 GB RAM.
I get the following crash report:
Node: mriqc_wf.dwiMRIQC.drift
Working directory: /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-04004..ses-01..dwi..sub-04004_ses-01_dir-PA_dwi.nii.gz/drift
Node inputs:
b0_ixs = [0, 1, 5, 18, 31, 46, 59, 72, 85, 98, 110, 119, 124]
bias_file = <undefined>
brainmask_file = /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/synthstrip_wf/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-04004..ses-01..dwi..sub-04004_ses-01_dir-PA_dwi.nii.gz/synthstrip/clipped_corrected_desc-brain_mask.nii.gz
bval_file = /fs03/wr47/cmar0007/FreeWater/SEL003_bids/sub-04004/ses-01/dwi/sub-04004_ses-01_dir-PA_dwi.bval
full_epi = /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-04004..ses-01..dwi..sub-04004_ses-01_dir-PA_dwi.nii.gz/sanitize/sub-04004_ses-01_dir-PA_dwi_valid.nii.gz
in_file = /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-04004..ses-01..dwi..sub-04004_ses-01_dir-PA_dwi.nii.gz/hmc_b0/sub-04004_ses-01_dir-PA_dwi_valid_subset_volreg.nii.gz
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 64, in run_node
result['result'] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node drift.
Traceback:
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/diffusion.py", line 597, in _run_interface
data = img.get_fdata()
^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/dataobj_images.py", line 373, in get_fdata
data = np.asanyarray(self._dataobj, dtype=dtype)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 457, in __array__
arr = self._get_scaled(dtype=dtype, slicer=())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 424, in _get_scaled
scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 394, in _get_unscaled
return array_from_file(
^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/volumeutils.py", line 472, in array_from_file
raise OSError(
OSError: Expected 28338336 bytes, got 6539616 bytes from object
- could the file be damaged?
Working directory: /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-04004..ses-01..dwi..sub-04004_ses-01_dir-PA_dwi.nii.gz/drift
Node inputs:
b0_ixs = [0, 1, 5, 18, 31, 46, 59, 72, 85, 98, 110, 119, 124]
bias_file = <undefined>
brainmask_file = /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/synthstrip_wf/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-04004..ses-01..dwi..sub-04004_ses-01_dir-PA_dwi.nii.gz/synthstrip/clipped_corrected_desc-brain_mask.nii.gz
bval_file = /fs03/wr47/cmar0007/FreeWater/SEL003_bids/sub-04004/ses-01/dwi/sub-04004_ses-01_dir-PA_dwi.bval
full_epi = /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-04004..ses-01..dwi..sub-04004_ses-01_dir-PA_dwi.nii.gz/sanitize/sub-04004_ses-01_dir-PA_dwi_valid.nii.gz
in_file = /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-04004..ses-01..dwi..sub-04004_ses-01_dir-PA_dwi.nii.gz/hmc_b0/sub-04004_ses-01_dir-PA_dwi_valid_subset_volreg.nii.gz
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 64, in run_node
result['result'] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node drift.
Traceback:
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/diffusion.py", line 597, in _run_interface
data = img.get_fdata()
^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/dataobj_images.py", line 373, in get_fdata
data = np.asanyarray(self._dataobj, dtype=dtype)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 457, in __array__
arr = self._get_scaled(dtype=dtype, slicer=())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 424, in _get_scaled
scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 394, in _get_unscaled
return array_from_file(
^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/volumeutils.py", line 472, in array_from_file
raise OSError(
OSError: Expected 28338336 bytes, got 6539616 bytes from object
- could the file be damaged?
I then tried increasing the memory to 100GB and got a similar error (although different file size) for a different subject:
Node: mriqc_wf.dwiMRIQC.drift
Working directory: /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-01006..ses-01..dwi..sub-01006_ses-01_dir-PA_dwi.nii.gz/drift
Node inputs:
b0_ixs = [0, 1, 5, 18, 31, 46, 59, 72, 85, 98, 110, 119, 124]
bias_file = <undefined>
brainmask_file = /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/synthstrip_wf/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-01006..ses-01..dwi..sub-01006_ses-01_dir-PA_dwi.nii.gz/synthstrip/clipped_corrected_desc-brain_mask.nii.gz
bval_file = /fs03/wr47/cmar0007/FreeWater/SEL003_bids/sub-01006/ses-01/dwi/sub-01006_ses-01_dir-PA_dwi.bval
full_epi = /fs03/wr47/cmar0007/FreeWater/SEL003_bids/sub-01006/ses-01/dwi/sub-01006_ses-01_dir-PA_dwi.nii.gz
in_file = /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-01006..ses-01..dwi..sub-01006_ses-01_dir-PA_dwi.nii.gz/hmc_b0/sub-01006_ses-01_dir-PA_dwi_subset_volreg.nii.gz
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 64, in run_node
result['result'] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node drift.
Traceback:
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/diffusion.py", line 597, in _run_interface
data = img.get_fdata()
^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/dataobj_images.py", line 373, in get_fdata
data = np.asanyarray(self._dataobj, dtype=dtype)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 457, in __array__
arr = self._get_scaled(dtype=dtype, slicer=())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 424, in _get_scaled
scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 394, in _get_unscaled
return array_from_file(
^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/volumeutils.py", line 472, in array_from_file
raise OSError(
OSError: Expected 28338336 bytes, got 10899360 bytes from object
- could the file be damaged?
Working directory: /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-01006..ses-01..dwi..sub-01006_ses-01_dir-PA_dwi.nii.gz/drift
Node inputs:
b0_ixs = [0, 1, 5, 18, 31, 46, 59, 72, 85, 98, 110, 119, 124]
bias_file = <undefined>
brainmask_file = /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/synthstrip_wf/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-01006..ses-01..dwi..sub-01006_ses-01_dir-PA_dwi.nii.gz/synthstrip/clipped_corrected_desc-brain_mask.nii.gz
bval_file = /fs03/wr47/cmar0007/FreeWater/SEL003_bids/sub-01006/ses-01/dwi/sub-01006_ses-01_dir-PA_dwi.bval
full_epi = /fs03/wr47/cmar0007/FreeWater/SEL003_bids/sub-01006/ses-01/dwi/sub-01006_ses-01_dir-PA_dwi.nii.gz
in_file = /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-01006..ses-01..dwi..sub-01006_ses-01_dir-PA_dwi.nii.gz/hmc_b0/sub-01006_ses-01_dir-PA_dwi_subset_volreg.nii.gz
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 64, in run_node
result['result'] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node drift.
Traceback:
Traceback (most recent call last):
File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/diffusion.py", line 597, in _run_interface
data = img.get_fdata()
^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/dataobj_images.py", line 373, in get_fdata
data = np.asanyarray(self._dataobj, dtype=dtype)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 457, in __array__
arr = self._get_scaled(dtype=dtype, slicer=())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 424, in _get_scaled
scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/arrayproxy.py", line 394, in _get_unscaled
return array_from_file(
^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.11/site-packages/nibabel/volumeutils.py", line 472, in array_from_file
raise OSError(
OSError: Expected 28338336 bytes, got 10899360 bytes from object
- could the file be damaged?
Could someone please assist with how I can resolve this?
Thank you
Oscar Esteban
May 20, 2024, 10:18:44 AM5/20/24
to Cassandra Marotta, mriqc-users
Dear Cassandra,
This looks like there was a previous error and for that reason, the realigned files are corrupted (e.g., /fs03/wr47/cmar0007/work/mriqc_wf/dwiMRIQC/_in_file_..fs03..wr47..cmar0007..FreeWater..SEL003_bids..sub-04004..ses-01..dwi..sub-04004_ses-01_dir-PA_dwi.nii.gz/hmc_b0/sub-04004_ses-01_dir-PA_dwi_valid_subset_volreg.nii.gz). May you be reaching the quota of the working directory's filesystem?
MRIQC should have generated a log in the output folder, could you share that with us?
Cheers,
oe
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Cassandra Marotta
May 21, 2024, 8:30:14 PM5/21/24
to mriqc-users
Hi Oscar,
Thank you for looking into this.
The working directory has a very large quota so I don't think that this is an issue. I have attached the logs that were output for both runs.
Kind regards,
Cassandra
Oscar Esteban
May 22, 2024, 5:24:23 AM5/22/24
to Cassandra Marotta, mriqc-users
Dear Cassandra,
It looks to me like you are re-using previously computed results, as I cannot find where the previous node (realignment) is executed. It seems to be pulled out of the cache. Can I ask you to completely wipe the working directory (/fs03/wr47/cmar0007/work/mriqc_wf) and try again?
I also cannot find the configuration of your execution. Can you share the config file (also in the output folder) and/or the command line you are using?
Cheers,
oe
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Cassandra Marotta
May 24, 2024, 4:58:18 AM5/24/24
to Oscar Esteban, mriqc-users
Thanks Oscar,
It looks like the previously computed files were the issue as after I deleted everything I was able to run through with no errors. Thank you so much for your help!
Kind regards,
Cassandra
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