Stuck at FreeSurfer Stage (mris_fix_topolo) #104
Comments
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Hi, @fullcream9. How many of the 400 subjects have this error? It looks like this could be an error with the field maps and/or field map jsons. Does this subject have field maps and if so, do the field map jsons contain intended for fields that match the field maps with the appropriate functional run files? Are the fmap or func files/jsons different somehow from the subjects you've been able to process successfully? |
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Hi, Thank you for your response and suggestions. I've carefully checked the fmap and func files/jsons for the failed subjects and found no difference between successful subjects. So far, I have processed 400 subjects in sequence and successfully completed 280 of them before encountering the error. So, about 120 subjects have this error. To pinpoint the problem, I attempted to process one subject, sub-NDARRR570MC0, individually using the following command:
It appears that the issue arises during the FreeSurfer recon-all step (mris_fix_topolo, in particular). I'm attaching the NDARRR570MC0_test_newserver.log and recon-all.err files for your reference and further insight. Any additional guidance or insights you could provide would be greatly appreciated. NDARRR570MC0_test_newserver.log: abcd-hcp-pipeline v0.1.3 recon-all.err：SUBJECT NDARRR570MC0 |
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@fullcream9 I'm so sorry this fell off my radar, I somehow never received a notification that you had responded. Are you still working on this? Off the top of my head:
I'm going to close this for now since it's been so long, but please open it again if you would like more help/have updates! Apologies again! |
What happened?
Dear abcd-hcp-pipeline Developers,
I am currently working on processing Human Brain Network (HBN) subjects and have encountered an issue with the abcd-hcp-pipeline version 0.1.3, specifically, I am stuck at the FreeSurfer stage. Specifically, the process seems to hang indefinitely during the execution of the "mris_fix_topolo" command. This issue is observed through the top command, which shows continuous execution without progression.
I am tasked with processing over 400 subjects and have successfully processed 286 of them before encountering this problem.
What command did you use?
What version of the abcd-hcp pipeline are you using?
abcd-hcp-pipeline v0.1.3
Directory Structure
No response
Relevant log output
abcd-hcp-pipeline v0.1.3 running FreeSurfer /opt/pipeline/FreeSurfer/FreeSurferPipeline.sh \ --subject=NDARRR570MC0 \ --subjectDIR=/output/sub-NDARRR570MC0/ses-None/files/T1w \ --t1=/output/sub-NDARRR570MC0/ses-None/files/T1w/T1w_acpc_dc_restore.nii.gz \ --t1brain=/output/sub-NDARRR570MC0/ses-None/files/T1w/T1w_acpc_dc_restore_brain.nii.gz \ --t2=/output/sub-NDARRR570MC0/ses-None/files/T1w/T2w_acpc_dc_restore.nii.gz \ --useT2=true \ --printcom= missing expected outputs from FreeSurfer file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/T1w_hires.nii.gz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/lh.EC_average file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/rh.EC_average file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/label/lh.aparc.a2009s.annot file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/label/lh.aparc.annot file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/label/rh.aparc.annot file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/T1w_hires.masked.mgz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/aparc+aseg.mgz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/aparc.a2009s+aseg.mgz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/aseg.hires.mgz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/aseg.hires.nii.gz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/brain.hires.mgz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/lh.ribbon.mgz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/rh.ribbon.mgz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/ribbon.mgz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/wm.hires.mgz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/mri/wmparc.mgz file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/stats/aseg.stats file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/stats/lh.aparc.a2009s.stats file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/stats/lh.aparc.stats file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/stats/lh.curv.stats file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/stats/rh.aparc.a2009s.stats file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/stats/rh.aparc.stats file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/stats/rh.curv.stats file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.area file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.area.mid file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.area.pial file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.area.prehires file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.curv file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.curv.pial file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.curv.prehires file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.pial file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.sphere file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.sphere.reg file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.sulc file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.thickness file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.volume file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.white file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.white.deformed file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/lh.white.prehires file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.area file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.area.mid file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.area.pial file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.curv file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.curv.pial file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.inflated file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.orig file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.pial file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.sphere file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.sphere.reg file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.sulc file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.thickness file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.volume file not found: /output/sub-NDARRR570MC0/ses-None/files/T1w/NDARRR570MC0/surf/rh.white Traceback (most recent call last): File "/app/run.py", line 397, in <module> _cli() File "/app/run.py", line 69, in _cli return interface(**kwargs) File "/app/run.py", line 393, in interface stage.run(ncpus) File "/app/pipelines.py", line 592, in run self.teardown(result) File "/app/pipelines.py", line 538, in teardown self.__class__.__name__) Exception: error caught during stage: FreeSurfer The pipeline must choose distortion correction method based on the type(s) of field maps available. The type of fieldmaps you have are either not able to be used in the abcd-hcp-pipeline or they are not properly identified in the BIDS format. The pipeline does not account for 'phasediff', 'magnitude', and 'fieldmap' field maps filetypes yet. If you have 'phasediff' and 'magnitude' field maps, please provide the original 'phase1', 'phase2', 'magnitude1', and 'magnitude2' field maps used to calculate those files. The pipeline does the calculation itself. /home/panshi/Documents/ABCD-BIDS/HBN_deri_temp/sub-NDARBE096YK6/ses-None/logs/FreeSurfer/status.json { "num_runs": 1, "node_status": 3, "comment": "stage terminated, some required files were not created." }Add any additional information or context about the problem here.
No response
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