Hi, I am using fmriprep to preprocess my data. I initially downloaded the public dataset (Flanker) online and processed it well using fmriprep. But when I tried to use my own dataset, an error occurred. The code shows ‘Runtime Error: Robust spatial normalization failed after 3 trials.’. Since the Flanker dataset is a normal human dataset and my dataset contains brain lesions, I suspect that this may be the reason for the normalization failure. I added the lesion_roi.nii file to my dataset, but in the end, Robust spatial normalization failed after 3 trials. Does anyone know what’s going on？
Command used (and if a helper script was used, a link to the helper script or the command generated):
It looks like there’s an extra _T1w in the file name for the lesion (should just be sub-001_label-lesion_roi.nii.gz). I’m not fixing that will make a difference, but can you do that and try again? When you rerun, can you specify a working directory (-w argument) so we can inspect those outputs, need be? Also, can you confirm the lesion ROI and T1w are well aligned with each other?
I will fix the name and add -w, thanks for your suggestion. As for the ROI and T1W alignment. I use ITK-SNAP to create a ROI by semi-supervised. This is the result and I think they align well.
No ROI
[Node] Error on “fmriprep_24_1_wf.sub_001_wf.anat_fit_wf.register_template_wf.registration” (/scratch/fmriprep_24_1_wf/sub_001_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin2009cAsym/registration)
2024-11-04 06:47:32,509 [ WARNING] [Node] Error on “fmriprep_24_1_wf.sub_001_wf.anat_fit_wf.register_template_wf.registration” (/scratch/fmriprep_24_1_wf/sub_001_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin2009cAsym/registration)
241104-06:47:34,304 nipype.workflow ERROR:
Node registration.a0 failed to run on host 24a586c5a0e1.
2024-11-04 06:47:34,304 [ ERROR] Node registration.a0 failed to run on host 24a586c5a0e1.
241104-06:47:34,324 nipype.workflow ERROR:
Saving crash info to /out/sub-001/log/20241104-055751_b3629f2d-fca4-44f7-bd82-bf46105fe0df/crash-20241104-064734-root-registration.a0-8266b613-26a8-43a6-9baa-02d6eb46cbcd.txt
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py”, line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py”, line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/opt/conda/envs/fmriprep/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 registration.
Traceback:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py”, line 397, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/opt/conda/envs/fmriprep/lib/python3.11/site-packages/niworkflows/interfaces/norm.py”, line 245, in _run_interface
raise RuntimeError(
RuntimeError: Robust spatial normalization failed after 3 retries.
It shows there is a registration problem from orignal T1 to MIN152, but I do not konw why this happen since if I use Flanker dataset it would run well without error. And this is the report in /scratch/fmriprep_24_1_wf/sub_001_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin2009cAsym/registration
