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The lesion extension is memory hungry. The exact amount of RAM memory depends
on the size and resolution of the scans.
I'd say you need almost 16GB for 1mm (256x256x256) scans.
Best,
Stefano
________________________________
From: Hoopes, Andrew <ahoo...@mgh.harvard.edu>
Sent: 10 May 2021 19:59
To: Freesurfer support list; Stefano Cerri
Subject: Re: [Freesurfer] Error in SAMSEG preprocessing
If this is the last message before crashing, it sounds like it’s probably a
memory issue – how much do you have available? CC’ing Stefano who might have an
idea of the total memory requirement for lesions.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro Leon
<bertocer...@gmail.com>
Date: Monday, May 10, 2021 at 9:31 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Error in SAMSEG preprocessing
External Email - Use Caution
After 14th interaction the terminal wrote this message:
I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports
instructions that this TensorFlow binary was not compiled to use: AVX2
2021-05-10 13:40:01.273046: I
tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency:
3292375000 Hz
2021-05-10 13:40:01.281440: I tensorflow/compiler/xla/service/service.cc:150]
XLA service 0x30013a0 executing computations on platform Host. Devices:
2021-05-10 13:40:01.281470: I tensorflow/compiler/xla/service/service.cc:158]
StreamExecutor device (0): <undefined>, <undefined>
WARNING:tensorflow:From
/usr/local/freesurfer/python/lib/python3.6/site-packages/tensorflow/python/training/saver.py:1266:
checkpoint_exists (from tensorflow.python.training.checkpoint_management) is
deprecated and will be removed in a future version.
Instructions for updating:
Use standard file APIs to check for files with this prefix.
VAE lesion model loaded
2021-05-10 13:40:16.471711: W tensorflow/core/framework/allocator.cc:124]
Allocation of 1717200000 exceeds 10% of system memory.
I tried to improve the system memory of my virtual machine but the same error
appeared.
Any suggestions?
El vie, 7 may 2021 a las 20:59, Hoopes, Andrew
(<ahoo...@mgh.harvard.edu<mailto:ahoo...@mgh.harvard.edu>>) escribió:
If the output directory is missing seg.mgz, then samseg failed. You’ll have to
send us the log or some sort of information about the error for us to debug
this.
Best
Andrew
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Alberto Del Cerro Leon
<bertocer...@gmail.com<mailto:bertocer...@gmail.com>>
Date: Friday, May 7, 2021 at 6:49 AM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Error in SAMSEG preprocessing
External Email - Use Caution
Hello, I am trying to use SAMSEG to segment white matter lesions, I ran the
following command:
run_samseg --input '/home/neuroimage/fsl/vascular/1002/U1002_3DT1.nii'
'/home/neuroimage/fsl/vascular/1002/flair_reg.nii' --pallidum-separate --lesion
--lesion-mask-pattern 0 1 --output '/home/neuroimage/fsl/vascular/1002/'
The output files were:
* cost.txt
* priors-testing.mgz
* samseg.talairach.lta
* template.lta
* template_coregistered.mgz
* template_transforms.mat
However I don't find any file with the white matter lesions segmented or a stat
file. I would send you the terminal outputs but is too extensive. Would you
help me?
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