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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?
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alberto Del Cerro Leon bertocerron@gmail.com Date: Friday, May 7, 2021 at 6:49 AM To: Freesurfer support list 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?
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 (AHOOPES@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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro Leon bertocerron@gmail.com *Date: *Friday, May 7, 2021 at 6:49 AM *To: *Freesurfer support list 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? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1TehWGCxNiuRHOQYLTB-oA6DCx2RK244h7Q5HWmIGXOtq0i... 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 http://secure-web.cisco.com/1QxYjqlRJPbxGmQ7muQI08i0E_Ta77Hs5RqkRdD6XGFGDUGX... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alberto Del Cerro Leon bertocerron@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 (<AHOOPES@mgh.harvard.edumailto:AHOOPES@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro Leon <bertocerron@gmail.commailto:bertocerron@gmail.com> Date: Friday, May 7, 2021 at 6:49 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1TehWGCxNiuRHOQYLTB-oA6DCx2RK244h7Q5HWmIGXOtq0iXjg6q9WpW_f9H3HcjQLpE3ZqBIz5W1OM3ZWjOMzYYFu8EbU8gxvZ46LC8fbZKMdqN1pU1jwjdU1ZcyoYIf4ntG6n-qx5bXb10fnhTYj2zpRa3ORuXZJMGCbp_VycdsrbMQhZFfQgO12omg0NNN8IU0Dug-Ss1IQhlPQvlbIwlQI14f3gaBTiZRw4bwSC-uDQCqwMBYWOjlqc_BsEfj/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.massgeneralbrigham.org/compliancelinehttp://secure-web.cisco.com/1QxYjqlRJPbxGmQ7muQI08i0E_Ta77Hs5RqkRdD6XGFGDUGXP83KZxoS_rb2lxEBnd2vYPGYQex2OG12SG5f411W7niZO3DLbxIzQMyPAiu2FNPbG2BFi9TReiANj4XGhgR6g5dp9xYMW01DmE9SOhIHNOXK4bvTPdlu51gZPyHAvNo9kYCbZIwyxF6ZdCe_pUObxKVUt_TSG7Yp2v9O0uPmLge3SO1ku7uiK8soWXkxKXdYs4b40nYDLzkBVQbZs/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
External Email - Use Caution
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 AHOOPES@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alberto Del Cerro Leon bertocerron@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 (<AHOOPES@mgh.harvard.edumailto:AHOOPES@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alberto Del Cerro Leon <bertocerron@gmail.commailto:bertocerron@gmail.com> Date: Friday, May 7, 2021 at 6:49 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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?
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14AFJPkeVi9akDn8KtOYPc3mLWTxeRgrsZ9lHJnrXFygD1j...https://secure-web.cisco.com/1TehWGCxNiuRHOQYLTB-oA6DCx2RK244h7Q5HWmIGXOtq0iXjg6q9WpW_f9H3HcjQLpE3ZqBIz5W1OM3ZWjOMzYYFu8EbU8gxvZ46LC8fbZKMdqN1pU1jwjdU1ZcyoYIf4ntG6n-qx5bXb10fnhTYj2zpRa3ORuXZJMGCbp_VycdsrbMQhZFfQgO12omg0NNN8IU0Dug-Ss1IQhlPQvlbIwlQI14f3gaBTiZRw4bwSC-uDQCqwMBYWOjlqc_BsEfj/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1BRRmyJGNu6EVODxd_FzCLxGjX7dmVXleiMIXnLuAy7KiMU8...http://secure-web.cisco.com/1QxYjqlRJPbxGmQ7muQI08i0E_Ta77Hs5RqkRdD6XGFGDUGXP83KZxoS_rb2lxEBnd2vYPGYQex2OG12SG5f411W7niZO3DLbxIzQMyPAiu2FNPbG2BFi9TReiANj4XGhgR6g5dp9xYMW01DmE9SOhIHNOXK4bvTPdlu51gZPyHAvNo9kYCbZIwyxF6ZdCe_pUObxKVUt_TSG7Yp2v9O0uPmLge3SO1ku7uiK8soWXkxKXdYs4b40nYDLzkBVQbZs/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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 http://secure-web.cisco.com/1BRRmyJGNu6EVODxd_FzCLxGjX7dmVXleiMIXnLuAy7KiMU8... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
freesurfer@nmr.mgh.harvard.edu
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Alberto Del Cerro Leon -
Hoopes, Andrew -
Stefano Cerri