Great! Can you please try processing the input scan with SuperSynth and sending me the output?
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Dear Eugenio,
many thanks for the quick response. Actually, it seems to me that your advice worked well.
Now, I have another issue: it could be some problem with SuperSynth. I re-downloaded today the file "SuperSynth_August_2025.pth".
Do you have any suggestions to solve the issue?
Thanks in advance,
Best wishes,
Vittorio
Running command:
fspython /Applications/freesurfer/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py --i /Users/disordinimovimento2/Documents/Vittorio/T1.nii.gz --o /Users/disordinimovimento2/Documents/Vittorio/prova_nextbrain --device cpu --side left --mode
invivo --atlas_dir /Applications/freesurfer/python/packages/ERC_bayesian_segmentation//atlas_simplified
GPU/CUDA not available; using the CPU
Using all available CPU threads ( 28 )
Warning: output directory exists
Current Time = 18:03:55
Analyzing image with SuperSynth...
Running command:
fspython /Applications/freesurfer/python/packages/SuperSynth//scripts/inference.py --i /Users/disordinimovimento2/Documents/Vittorio/T1.nii.gz --o /Users/disordinimovimento2/Documents/Vittorio/prova_nextbrain/SuperSynth/ --mode invivo --threads 28 --device
cpu --model_file /Applications/freesurfer/models/SuperSynth_August_2025.pth --test_time_flipping
/Applications/freesurfer/python/packages/SuperSynth//scripts/inference.py:40: DeprecationWarning: Please use `binary_dilation` from the `scipy.ndimage` namespace, the `scipy.ndimage.morphology` namespace is deprecated.
from scipy.ndimage.morphology import binary_dilation
It seems like your input is an image file
/Applications/freesurfer/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/torch/amp/autocast_mode.py:250: UserWarning: User provided device_type of 'cuda', but CUDA is not available. Disabling
warnings.warn(
Preparing model and loading weights
Preparing model and loading weights
Working on image 1 of 1: /Users/disordinimovimento2/Documents/Vittorio/T1.nii.gz
Mode is: invivo
Reading, resampling, and padding input image
Pushing data through the CNN
/Applications/freesurfer/bin/mri_super_synth: line 86: 14594 Killed: 9 fspython /Applications/freesurfer/python/packages/SuperSynth//scripts/inference.py --i /Users/disordinimovimento2/Documents/Vittorio/T1.nii.gz --o /Users/disordinimovimento2/Documents/Vittorio/prova_nextbrain/SuperSynth/
--mode invivo --threads 28 --device cpu --model_file /Applications/freesurfer/models/SuperSynth_August_2025.pth --test_time_flipping
Traceback (most recent call last):
File "/Applications/freesurfer/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py", line 174, in <module>
raise Exception('Problem with SuperSynth; exitting...')
Exception: Problem with SuperSynth; exitting...
Dear Vittorio,
This is pretty weird… you could in principle fix this by running
fspython -m pip install opencv-python
but the error is probably sign of a wider problem so you’re probably better off installing the latest dev.
Best wishes,
/Eugenio
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Dear all,
I successfully downloaded the atlas, but when I try to run the segmentation tool, I have the following error. Could you help me please?
Best regards
Vittorio
disordinimovimento2@Disordini-Movimento-2 ~ % mri_histo_atlas_segment_fireants --i/Users/disordinimovimento2/Documents/Vittorio/T1.nii.gz --o /Users/disordinimovimento2/Documents/Vittorio/prova_nextbrain --device cpu --side left --mode invivo
Running command:
fspython /Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py --i/Users/disordinimovimento2/Documents/Vittorio/T1.nii.gz --o /Users/disordinimovimento2/Documents/Vittorio/prova_nextbrain --device cpu --side left
--mode invivo --atlas_dir /Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation//atlas_simplified
Traceback (most recent call last):
File "/Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation//scripts/segment_fireants.py", line 9, in <module>
import ext.my_functions as my
File "/Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation/ext/my_functions.py", line 4, in <module>
import cv2
ModuleNotFoundError: No module named 'cv2'
disordinimovimento2@Disordini-Movimento-2 ~ %