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

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...

Il giorno mar 3 mar 2026 alle ore 22:20 Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> ha scritto:

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

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

From: Vittorio Rispoli <vit.rispoli@gmail.com>
Date: Tuesday, March 3, 2026 at 4:47 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] nextbrain segmentation tool issue

External Email - Use Caution

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 ~ %

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