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Hello FreeSurfer Developers,
I encountered an error during the mri_sclimbic_seg step while performing cortical segmentation and surface reconstruction using FreeSurfer version 8.1's recon-all command. The program terminated unexpectedly at this stage.
mri_sclimbic_seg --model /models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/invol.lh.crop.nii.gz --o /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/seg.lh.mgz Traceback (most recent call last): File "/usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg", line 1077, in <module> main() File "/usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg", line 170, in main /usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg --model /models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/invol.lh.crop.nii.gz --o /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/seg.lh.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /data2/FST1T2Res/002_S_0295_006/mri/tmp.mri_mcadura_seg.271283/dumca.lh.ctab Loaded population stats /usr/local/freesurfer/8.1.0/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- segmenter = LimbicSegmenter(model_file=model_file, File "/usr/local/freesurfer/8.1.0/python/scripts/mri_sclimbic_seg", line 425, in __init__ self.model.load_weights(model_file, by_name=True) File "/usr/local/freesurfer/8.1.0/python/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 70, in error_handler raise e.with_traceback(filtered_tb) from None File "/usr/local/freesurfer/8.1.0/python/lib/python3.8/site-packages/h5py/_hl/files.py", line 562, in __init__ fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr) File "/usr/local/freesurfer/8.1.0/python/lib/python3.8/site-packages/h5py/_hl/files.py", line 235, in make_fid fid = h5f.open(name, flags, fapl=fapl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 102, in h5py.h5f.open FileNotFoundError: [Errno 2] Unable to synchronously open file (unable to open file: name = '/models/mca-dura.both-lh.nstd21.fhs.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the recon-all.log in case it's of any use.
1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-8.1.0-20250718-f30dfed 2) Platform: Ubuntu 20.04 3) uname -a: Linux synmr-X12DPi-N-T-6 5.15.0-139-generic #149~20.04.1-Ubuntu SMP Wed Apr 16 08:29:56 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached
-- Sung-Ho Woo Research Professor, Dongguk University
tel : 82-31-961-5744 mobile : 82-10-3746-6124 e-mail : nalwsh@gmail.com / nalwsh@dongguk.edu