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 ~ %
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 ~ %
External Email - Use Caution
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...
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://secure-web.cisco.com/1f8157GO7CRo5PKb_jZ8xsgeHfcRKP5BHw6z1m4wjDau2X2N... *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 myFile "/Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation/ext/my_functions.py", line 4, in <module>
import cv2ModuleNotFoundError: No module named 'cv2'
disordinimovimento2@Disordini-Movimento-2 ~ % _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
https://secure-web.cisco.com/16tNv7cT0oydxS9wSfZ3Ek9HHi5L37B6m9TJbJhKHgpV8zk... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1yO1F2Oh4yy1ZjErk1WHRNhnTBIIDS3aZ_G6IvR1icaZ0Yh... < https://secure-web.cisco.com/1yO1F2Oh4yy1ZjErk1WHRNhnTBIIDS3aZ_G6IvR1icaZ0Yh... .
Great! Can you please try processing the input scan with SuperSynth and sending me the output? https://surfer.nmr.mgh.harvard.edu/fswiki/SuperSynth
-- Juan Eugenio Iglesias http://www.jeiglesias.com From: Vittorio Rispoli vit.rispoli@gmail.com Date: Wednesday, March 4, 2026 at 12:51 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Re: nextbrain segmentation tool issue
External Email - Use Caution 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...
Il giorno mar 3 mar 2026 alle ore 22:20 Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edumailto: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.comhttp://secure-web.cisco.com/1f8157GO7CRo5PKb_jZ8xsgeHfcRKP5BHw6z1m4wjDau2X2NozSEL3AUk3hS9o53gTWxJUsN0wiRlUCSykw45pc0oxWfuyB1J1Cq2dS1_dgO3pQXoDFeIZXkv2Yasa8J9lkstFeFnoetBii53vq_OYMbvkWksZcexRJqS8xcd9dr050_ips5h5ZbIUqfjFVP3GizVv8IkozyB0NgdqDDBzkJsb0H_sWJWEZi6fNW6C_b3MERniKYCC3vIkceLtvyamzRHaZ8qkq3i8IplYFWL_4GLWLxUMeNQldnj3M8mdzGhPO7z8NrsgMAWBKOkVHIi5eN95eaI4lSLhpQ56Y4oUQ/http%3A%2F%2Fwww.jeiglesias.com From: Vittorio Rispoli <vit.rispoli@gmail.commailto:vit.rispoli@gmail.com> Date: Tuesday, March 3, 2026 at 4:47 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto: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 ~ %
_______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edumailto:freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...https://secure-web.cisco.com/16tNv7cT0oydxS9wSfZ3Ek9HHi5L37B6m9TJbJhKHgpV8zkij0uwIZm_QoVPzxv7t1bNjYnbEwa8jfbj7YZXbRSK5pZUSw7wZD2nrRDk9DykbE0voVKjlejNnQMnTmmnXEb8pZPkG-tGPzY7hYptWJc6IJjQggUx_fB-JTaNIWYYFbtC5lJeuQ19gIa4A1rFUD5dRjuUtuqtLQUIhcVxqhhTTRtdcnQbcCL9YWjR7DUzDTDLh8s3OEt7gclqwViMoTg3mfUE4bPz8rMbzpcnOfmA0g2sxA4WEmYemps_HUOt9CO_5_ghYnVr5qDyo5-NPldLQ1gWDYVppXah9tzAmqw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1yO1F2Oh4yy1ZjErk1WHRNhnTBIIDS3aZ_G6IvR1icaZ0YhHhFSP1mckO7T5NXZkvDsWa145OMRIG8GJMFj1CdjoASy8L7XqNjjmH2lbVL6xqtVDUw6KOoKNwzBL_duTTy1dQK2S2yE_-JXxdz9Hqre97RQuhpKWhcDC47tTxi7NemJnp-h3HzbcVcQGeeH_I7285EQPO9tDNigai3aAUX05zo8NuFNP_WpDvdySDuMiDCiprazfxq-2IOQW_F19pEhk1r2BMzsVINyveEOYSTMWykVFdLeFg4BBud-2UhG4cjOBn3TWos4muQus9ko4YwT3ZWS3wmfj6wekm1PTYmQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1yO1F2Oh4yy1ZjErk1WHRNhnTBIIDS3aZ_G6IvR1icaZ0YhHhFSP1mckO7T5NXZkvDsWa145OMRIG8GJMFj1CdjoASy8L7XqNjjmH2lbVL6xqtVDUw6KOoKNwzBL_duTTy1dQK2S2yE_-JXxdz9Hqre97RQuhpKWhcDC47tTxi7NemJnp-h3HzbcVcQGeeH_I7285EQPO9tDNigai3aAUX05zo8NuFNP_WpDvdySDuMiDCiprazfxq-2IOQW_F19pEhk1r2BMzsVINyveEOYSTMWykVFdLeFg4BBud-2UhG4cjOBn3TWos4muQus9ko4YwT3ZWS3wmfj6wekm1PTYmQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
External Email - Use Caution
For sure, I will run it tomorrow morning Best wishes Vittorio
Il Mer 4 Mar 2026, 19:52 Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> ha scritto:
Great! Can you please try processing the input scan with SuperSynth and sending me the output? https://secure-web.cisco.com/1duxfak9LBLkYwNNZRasoGYVQ0x1Ev-WBl0S3ANfxLXQ6Xw...
--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1dYnqbfp47HeIaiX-wJFLZFOi-aAAIuO_8-T9T8XxJEHNqIr... *From: *Vittorio Rispoli vit.rispoli@gmail.com *Date: *Wednesday, March 4, 2026 at 12:51 PM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Re: nextbrain segmentation tool issue
External Email - Use Caution *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...
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://secure-web.cisco.com/1dYnqbfp47HeIaiX-wJFLZFOi-aAAIuO_8-T9T8XxJEHNqIr... http://secure-web.cisco.com/1f8157GO7CRo5PKb_jZ8xsgeHfcRKP5BHw6z1m4wjDau2X2NozSEL3AUk3hS9o53gTWxJUsN0wiRlUCSykw45pc0oxWfuyB1J1Cq2dS1_dgO3pQXoDFeIZXkv2Yasa8J9lkstFeFnoetBii53vq_OYMbvkWksZcexRJqS8xcd9dr050_ips5h5ZbIUqfjFVP3GizVv8IkozyB0NgdqDDBzkJsb0H_sWJWEZi6fNW6C_b3MERniKYCC3vIkceLtvyamzRHaZ8qkq3i8IplYFWL_4GLWLxUMeNQldnj3M8mdzGhPO7z8NrsgMAWBKOkVHIi5eN95eaI4lSLhpQ56Y4oUQ/http%3A%2F%2Fwww.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 myFile "/Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation/ext/my_functions.py", line 4, in <module>
import cv2ModuleNotFoundError: No module named 'cv2'
disordinimovimento2@Disordini-Movimento-2 ~ % _______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
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External Email - Use Caution
Dear Eugenio, thanks again for your help. Actually, the issue seemed related to computational power. Yesterday, the machine where I previously ran the tool was busy. So, I used another machine with more RAM and it works. Just a quick question, looking at the segmentation and volume output, I do not see the segmentation of cerebellar cortex and dentate nucleus. Is this correct? should I do something different to also have the segmentation of cerebellar cortex and dentate nucleus? Please, find the outputs of the right h in the attached files. Thanks in advance Vittorio
Il giorno mer 4 mar 2026 alle ore 19:52 Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> ha scritto:
Great! Can you please try processing the input scan with SuperSynth and sending me the output? https://secure-web.cisco.com/14Sy25Ls5MUm_uvzO30iNurbYZgYjsFYZm9-HSht5kpIvgR...
--
Juan Eugenio Iglesias
http://secure-web.cisco.com/1Zfrzy19I-pfZnfh_wMW52_4Br3YVwGbrLx1RgMnXfjWK-iJ... *From: *Vittorio Rispoli vit.rispoli@gmail.com *Date: *Wednesday, March 4, 2026 at 12:51 PM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Re: nextbrain segmentation tool issue
External Email - Use Caution *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...
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
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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 myFile "/Applications/freesurfer/dev/python/packages/ERC_bayesian_segmentation/ext/my_functions.py", line 4, in <module>
import cv2ModuleNotFoundError: No module named 'cv2'
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freesurfer@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Juan E. -
Vittorio Rispoli