MRIQC for LF-MRI

[HengamehMarzbani]

What happened?

Hello,

I want to use MRIQC for low-field MRI data (T1W and T2W) that has been BIDS-ified. I am encountering this error. Would you please guide me on how to fix it?

INFO:    Converting SIF file to temporary sandbox...
Traceback (most recent call last):
  File "/opt/conda/bin/mriqc", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/lib/python3.9/site-packages/mriqc/cli/run.py", line 168, in main
    mriqc_wf.run(**_plugin)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 184, in run
    self._clean_queue(jobid, graph, result=result)
  File "/opt/conda/lib/python3.9/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/python3.9/site-packages/mriqc/engine/plugin.py", line 60, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/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 measures.

Traceback:
    Traceback (most recent call last):
      File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 397, in run
        runtime = self._run_interface(runtime)
      File "/opt/conda/lib/python3.9/site-packages/mriqc/interfaces/anatomical.py", line 114, in _run_interface
        raise RuntimeError(
    RuntimeError: Input inhomogeneity-corrected data seem empty. MRIQC failed to process this dataset.

INFO:    Cleaning up image...

What command did you use?

singularity run --home ${HOME_DIR} -B ${TEMPLATEFLOW_HOME:${WRITE_DIR}/.cache/templateflow}:${TEMPL_HOME} ${IMAGE_LOC} "${BIDS_DIR}" "${DERIVS_DIR}" --nprocs 32 --omp-nthreads 32 --mem_gb 50 participant --participant-label ${subject} -m T1w T2w -w ${WORK_DIR} --no-sub

What version of the software are you running?

mriqc 23.1.0

How are you running this software?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

subject number: 030
230930-18:52:59,958 cli IMPORTANT:

    Running MRIQC version 23.1.0:
      * BIDS dataset path: .../bids.
      * Output folder: .../MRIQC.
      * Analysis levels: ['participant'].

230930-18:54:32,790 nipype.workflow WARNING:
     Storing result file without outputs
230930-18:54:32,792 nipype.workflow WARNING:
     [Node] Error on "mriqc_wf.anatMRIQC.ComputeIQMs.measures" (.../work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_......bids..sub-030..ses-t0..anat..sub-030_ses-t0_acq-cor_T1w.nii.gz/measures)
230930-18:54:32,856 nipype.workflow WARNING:
     Storing result file without outputs
230930-18:54:32,858 nipype.workflow WARNING:
     [Node] Error on "mriqc_wf.anatMRIQC.ComputeIQMs.measures" (.../work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_......bids..sub-030..ses-t0..anat..sub-030_ses-t0_acq-sag_T1w.nii.gz/measures)
230930-18:54:32,937 nipype.workflow WARNING:
     Storing result file without outputs
230930-18:54:32,940 nipype.workflow WARNING:
     [Node] Error on "mriqc_wf.anatMRIQC.ComputeIQMs.measures" (.../work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_......bids..sub-030..ses-t0..anat..sub-030_ses-t0_acq-axi_T2w.nii.gz/measures)
230930-18:54:33,29 nipype.workflow WARNING:
     Storing result file without outputs
230930-18:54:33,32 nipype.workflow WARNING:
     [Node] Error on "mriqc_wf.anatMRIQC.ComputeIQMs.measures" (.../work/mriqc_wf/anatMRIQC/ComputeIQMs/_in_file_......bids..sub-030..ses-t0..anat..sub-030_ses-t0_acq-cor_T2w.nii.gz/measures)
230930-18:54:34,455 nipype.workflow ERROR:
     Node measures.a1 failed to run on host se412.
230930-18:54:34,456 nipype.workflow ERROR:
     Saving crash info to .../MRIQC/logs/crash-20230930-185434-,,,-measures.a1-f81920d1-b742-497c-bd6f-b71949c2a1f3.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 60, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/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 measures.

Traceback:
    Traceback (most recent call last):
      File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 397, in run
        runtime = self._run_interface(runtime)
      File "/opt/conda/lib/python3.9/site-packages/mriqc/interfaces/anatomical.py", line 114, in _run_interface
        raise RuntimeError(
    RuntimeError: Input inhomogeneity-corrected data seem empty. MRIQC failed to process this dataset.

Additional information / screenshots

No response

[HengamehMarzbani]

Hello, I would be grateful if someone could answer my question. I have resolved the previous error. Now, I have .nii files for which I don't have their .json files. I was wondering if the "--skip-bids-validation" option does not work for MRIQC?

[celprov]

Hello @HengamehMarzbani, Could you share how you solved the error RuntimeError: Input inhomogeneity-corrected data seem empty? MRIQC failed to process this dataset. ? The same error was reported in #1142

Regarding your second question, I need more precise information to help you. You don't have the .json files associated with the .nii files in the input dataset or in the derivatives of MRIQC?

[HengamehMarzbani]

Hello,

Regarding the RuntimeError error for my dataset, I possessed the LF-MRI dataset, which lacked an ISO file. This implies that I had axial, sagittal, and coronal images for T1w. So, MRIQC runs effectively with images that have been registered across sagittal, axial, and coronal planes, and I do possess an ISO image (Just one T1w image with the three views).

About the error that was reported in #1142, it may be due to running out of disk space.

Regards Henagmeh

On Thu, Oct 12, 2023 at 4:20 PM celprov @.***> wrote:

Hello @HengamehMarzbani https://github.com/HengamehMarzbani, Could you share how you solved the error RuntimeError: Input inhomogeneity-corrected data seem empty? MRIQC failed to process this dataset. ? The same error was reported in #1142 https://github.com/nipreps/mriqc/issues/1142

Regarding your second question, I would interpret the absence of .json files as a sign that MRIQC did not successfully run until the end, but I need more precise information to help you out more on this.

— Reply to this email directly, view it on GitHub https://github.com/nipreps/mriqc/issues/1146#issuecomment-1760521465, or unsubscribe https://github.com/notifications/unsubscribe-auth/AXJW2XMKYMZY4NAZQUROJSLX7B3L5ANCNFSM6AAAAAA5OD7I2U . You are receiving this because you were mentioned.Message ID: @.***>

[oesteban]

This implies that I had axial, sagittal, and coronal images for T1w.

This is to say that you had 3 planes (e.g., like a localizer or what DL people call 2.5D) or that you had the three possible readout directions?

[oesteban]

This issue has been inactive for long. Please reopen if further action is necessary.