Open ZZLXY opened 2 months ago
Zhengwang-Wu
commented
2 months ago @ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208.
ZZLXY
commented
2 months ago @ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version
docker pull ibeatgroup/ ibeat_v2:release208.
Thank you very much for providing the latest version. Unfortunately, the issue persists. Specifically, I am still encountering the following error: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." I have provided the full command output above.
And I guess the printed output, "Smoothing volume: ............................................................." , is not normal? But I don't know what is the reason of this issue.
Additionally, I am using an RTX 4090 with CUDA 11.8.
Could you kindly advise on how to resolve this issue? Your assistance would be greatly appreciated.
iBEAT-V2
commented
2 months ago Interesting.
Can you share one sample for us to debug?
Thanks.
From: BrainResearcher @.> Date: Thursday, September 12, 2024 at 10:10 PM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Subscribed @.***> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5)
@ZZLXYhttps://github.com/ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208.
Thank you very much for providing the latest version. Unfortunately, the same issue has occurred again. Specifically, I am still encountering the error described above: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map."
Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance.
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2347904959, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2IKY3Q6KG55CFYEQXLZWJCSTAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBXHEYDIOJVHE. You are receiving this because you are subscribed to this thread.Message ID: @.***>
ZZLXY
commented
2 months ago Interesting. Can you share one sample for us to debug? Thanks. From: BrainResearcher @.> Date: Thursday, September 12, 2024 at 10:10 PM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Subscribed @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) @ZZLXYhttps://github.com/ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208. Thank you very much for providing the latest version. Unfortunately, the same issue has occurred again. Specifically, I am still encountering the error described above: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. — Reply to this email directly, view it on GitHub<#5 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2IKY3Q6KG55CFYEQXLZWJCSTAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBXHEYDIOJVHE. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response!
Actually, I have tested the tool on two datasets. Given that the same issue persists across different datasets, I suspect the problem may not be data-specific.
If it would help, I can provide sample data via email for your further investigation.
Thank you again for your continued assistance!
iBEAT-V2
commented
2 months ago Yes, one sample please.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 7:54 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5)
Interesting. Can you share one sample for us to debug? Thanks. From: BrainResearcher @.> Date: Thursday, September 12, 2024 at 10:10 PM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Subscribed @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5) @ZZLXYhttps://github.com/ZZLXYhttps://github.com/ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208. Thank you very much for providing the latest version. Unfortunately, the same issue has occurred again. Specifically, I am still encountering the error described above: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. — Reply to this email directly, view it on GitHub<#5 (comment)https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2347904959>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2IKY3Q6KG55CFYEQXLZWJCSTAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBXHEYDIOJVHE. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response!
Actually, I have tested the tool on two datasets. Given that the same issue persists across different datasets, I suspect the problem may not be data-specific.
If it would help, I can provide sample data via email for your further investigation.
Thank you again for your continued assistance!
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348775436, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2OJBRB23MQ24E6HFR3ZWLG6VAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG43TKNBTGY. You are receiving this because you commented.Message ID: @.***>
ZZLXY
commented
2 months ago Okay~
The sample data is attached to this email. Thank you very much!
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 19:56 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | Yes, one sample please.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 7:54 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5)
Interesting. Can you share one sample for us to debug? Thanks. From: BrainResearcher @.> Date: Thursday, September 12, 2024 at 10:10 PM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Subscribed @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5) @ZZLXYhttps://github.com/ZZLXYhttps://github.com/ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208. Thank you very much for providing the latest version. Unfortunately, the same issue has occurred again. Specifically, I am still encountering the error described above: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. — Reply to this email directly, view it on GitHub<#5 (comment)https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2347904959>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2IKY3Q6KG55CFYEQXLZWJCSTAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBXHEYDIOJVHE. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response!
Actually, I have tested the tool on two datasets. Given that the same issue persists across different datasets, I suspect the problem may not be data-specific.
If it would help, I can provide sample data via email for your further investigation.
Thank you again for your continued assistance!
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348775436, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2OJBRB23MQ24E6HFR3ZWLG6VAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG43TKNBTGY. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
iBEAT-V2
commented
2 months ago There is no attachment. Maybe a link should be fine.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:07 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Okay~
The sample data is attached to this email. Thank you very much!
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 19:56 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | Yes, one sample please.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 7:54 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5)
Interesting. Can you share one sample for us to debug? Thanks. From: BrainResearcher @.> Date: Thursday, September 12, 2024 at 10:10 PM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Subscribed @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5) @ZZLXYhttps://github.com/ZZLXYhttps://github.com/ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208. Thank you very much for providing the latest version. Unfortunately, the same issue has occurred again. Specifically, I am still encountering the error described above: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. — Reply to this email directly, view it on GitHub<#5 (comment)https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2347904959>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2IKY3Q6KG55CFYEQXLZWJCSTAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBXHEYDIOJVHE. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response!
Actually, I have tested the tool on two datasets. Given that the same issue persists across different datasets, I suspect the problem may not be data-specific.
If it would help, I can provide sample data via email for your further investigation.
Thank you again for your continued assistance!
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348775436, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2OJBRB23MQ24E6HFR3ZWLG6VAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG43TKNBTGY. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348797914, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2MMPXDZ5ZUSFI544ZLZWLIONAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG44TOOJRGQ. You are receiving this because you commented.Message ID: @.***>
ZZLXY
commented
2 months ago Could you please provide me with a personal email address? It might be more suitable for data sharing.
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 20:18 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | There is no attachment. Maybe a link should be fine.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:07 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Okay~
The sample data is attached to this email. Thank you very much!
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 19:56 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | Yes, one sample please.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 7:54 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5)
Interesting. Can you share one sample for us to debug? Thanks. From: BrainResearcher @.> Date: Thursday, September 12, 2024 at 10:10 PM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Subscribed @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5) @ZZLXYhttps://github.com/ZZLXYhttps://github.com/ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208. Thank you very much for providing the latest version. Unfortunately, the same issue has occurred again. Specifically, I am still encountering the error described above: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. — Reply to this email directly, view it on GitHub<#5 (comment)https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2347904959>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2IKY3Q6KG55CFYEQXLZWJCSTAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBXHEYDIOJVHE. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response!
Actually, I have tested the tool on two datasets. Given that the same issue persists across different datasets, I suspect the problem may not be data-specific.
If it would help, I can provide sample data via email for your further investigation.
Thank you again for your continued assistance!
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348775436, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2OJBRB23MQ24E6HFR3ZWLG6VAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG43TKNBTGY. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348797914, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2MMPXDZ5ZUSFI544ZLZWLIONAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG44TOOJRGQ. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
iBEAT-V2
commented
2 months ago Email:
@.**@.> @.**@.> @.**@.>
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:22 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Could you please provide me with a personal email address? It might be more suitable for data sharing.
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 20:18 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | There is no attachment. Maybe a link should be fine.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:07 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Okay~
The sample data is attached to this email. Thank you very much!
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 19:56 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | Yes, one sample please.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 7:54 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5)
Interesting. Can you share one sample for us to debug? Thanks. From: BrainResearcher @.> Date: Thursday, September 12, 2024 at 10:10 PM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Subscribed @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5) @ZZLXYhttps://github.com/ZZLXYhttps://github.com/ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208. Thank you very much for providing the latest version. Unfortunately, the same issue has occurred again. Specifically, I am still encountering the error described above: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. — Reply to this email directly, view it on GitHub<#5 (comment)https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2347904959>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2IKY3Q6KG55CFYEQXLZWJCSTAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBXHEYDIOJVHE. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response!
Actually, I have tested the tool on two datasets. Given that the same issue persists across different datasets, I suspect the problem may not be data-specific.
If it would help, I can provide sample data via email for your further investigation.
Thank you again for your continued assistance!
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348775436, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2OJBRB23MQ24E6HFR3ZWLG6VAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG43TKNBTGY. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348797914, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2MMPXDZ5ZUSFI544ZLZWLIONAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG44TOOJRGQ. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348827223, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2LF2OKCGW2LOTG4W7TZWLKHDAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYHAZDOMRSGM. You are receiving this because you commented.Message ID: @.***>
iBEAT-V2
commented
2 months ago Next time, if you encounter any errors or bugs, please send us the log file along with the testing subject for efficient troubleshooting. No need to send so many emails back and forth.
Thanks.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:22 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Could you please provide me with a personal email address? It might be more suitable for data sharing.
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 20:18 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | There is no attachment. Maybe a link should be fine.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:07 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Okay~
The sample data is attached to this email. Thank you very much!
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 19:56 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | Yes, one sample please.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 7:54 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5)
Interesting. Can you share one sample for us to debug? Thanks. From: BrainResearcher @.> Date: Thursday, September 12, 2024 at 10:10 PM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Subscribed @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5) @ZZLXYhttps://github.com/ZZLXYhttps://github.com/ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208. Thank you very much for providing the latest version. Unfortunately, the same issue has occurred again. Specifically, I am still encountering the error described above: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. — Reply to this email directly, view it on GitHub<#5 (comment)https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2347904959>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2IKY3Q6KG55CFYEQXLZWJCSTAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBXHEYDIOJVHE. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response!
Actually, I have tested the tool on two datasets. Given that the same issue persists across different datasets, I suspect the problem may not be data-specific.
If it would help, I can provide sample data via email for your further investigation.
Thank you again for your continued assistance!
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348775436, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2OJBRB23MQ24E6HFR3ZWLG6VAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG43TKNBTGY. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348797914, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2MMPXDZ5ZUSFI544ZLZWLIONAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG44TOOJRGQ. You are receiving this because you commented.Message ID: @.***>
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ZZLXY
commented
2 months ago Can you download it from the following link?
Link: https://pan.baidu.com/s/1WB2Mm7ow8uF8PRaNLCf90w
Extraction code: i8c0
These email addresses you provided have been anonymized. I sincerely apologize for any inconvenience this may have caused and truly appreciate your help!
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 20:26 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | Next time, if you encounter any errors or bugs, please send us the log file along with the testing subject for efficient troubleshooting. No need to send so many emails back and forth.
Thanks.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:22 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Could you please provide me with a personal email address? It might be more suitable for data sharing.
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 20:18 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | There is no attachment. Maybe a link should be fine.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:07 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Okay~
The sample data is attached to this email. Thank you very much!
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 19:56 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | Yes, one sample please.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 7:54 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5)
Interesting. Can you share one sample for us to debug? Thanks. From: BrainResearcher @.> Date: Thursday, September 12, 2024 at 10:10 PM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Subscribed @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5) @ZZLXYhttps://github.com/ZZLXYhttps://github.com/ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208. Thank you very much for providing the latest version. Unfortunately, the same issue has occurred again. Specifically, I am still encountering the error described above: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. — Reply to this email directly, view it on GitHub<#5 (comment)https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2347904959>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2IKY3Q6KG55CFYEQXLZWJCSTAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBXHEYDIOJVHE. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response!
Actually, I have tested the tool on two datasets. Given that the same issue persists across different datasets, I suspect the problem may not be data-specific.
If it would help, I can provide sample data via email for your further investigation.
Thank you again for your continued assistance!
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348775436, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2OJBRB23MQ24E6HFR3ZWLG6VAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG43TKNBTGY. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348797914, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2MMPXDZ5ZUSFI544ZLZWLIONAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG44TOOJRGQ. You are receiving this because you commented.Message ID: @.***>
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iBEAT-V2
commented
2 months ago It is too slow.
You can find my emails: https://liwang.web.unc.edu/contact/ Please send me the attachments using your email.
Thanks.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:53 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Can you download it from the following link?
Link: https://pan.baidu.com/s/1WB2Mm7ow8uF8PRaNLCf90w
Extraction code: i8c0
These email addresses you provided have been anonymized. I sincerely apologize for any inconvenience this may have caused and truly appreciate your help!
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 20:26 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | Next time, if you encounter any errors or bugs, please send us the log file along with the testing subject for efficient troubleshooting. No need to send so many emails back and forth.
Thanks.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:22 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Could you please provide me with a personal email address? It might be more suitable for data sharing.
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 20:18 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | There is no attachment. Maybe a link should be fine.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 8:07 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) Okay~
The sample data is attached to this email. Thank you very much!
| 896275822 | |
|---|---|
@. | ---- Replied Message ---- | From | iBEAT V2.0 @.> | | Date | 9/13/2024 19:56 | | To | @.> | | Cc | @.>, @.***> | | Subject | Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5) | Yes, one sample please.
From: BrainResearcher @.> Date: Friday, September 13, 2024 at 7:54 AM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Wang, Li @.>, Comment @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5)
Interesting. Can you share one sample for us to debug? Thanks. From: BrainResearcher @.> Date: Thursday, September 12, 2024 at 10:10 PM To: iBEAT-V2/iBEAT-V2.0-Docker @.> Cc: Subscribed @.> Subject: Re: [iBEAT-V2/iBEAT-V2.0-Docker] Error!!! Brain volume equals to 0 (Issue #5https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5) @ZZLXYhttps://github.com/ZZLXYhttps://github.com/ZZLXY The temporary file issue has been solved in a later version. Also, we have updated the segmentation model. Can you try the latest version docker pull ibeatgroup/ ibeat_v2:release208. Thank you very much for providing the latest version. Unfortunately, the same issue has occurred again. Specifically, I am still encountering the error described above: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. — Reply to this email directly, view it on GitHub<#5 (comment)https://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2347904959>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2IKY3Q6KG55CFYEQXLZWJCSTAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBXHEYDIOJVHE. You are receiving this because you are subscribed to this thread.Message ID: @.>
Thank you for your response!
Actually, I have tested the tool on two datasets. Given that the same issue persists across different datasets, I suspect the problem may not be data-specific.
If it would help, I can provide sample data via email for your further investigation.
Thank you again for your continued assistance!
— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348775436, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2OJBRB23MQ24E6HFR3ZWLG6VAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYG43TKNBTGY. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>
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— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348827223, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2LF2OKCGW2LOTG4W7TZWLKHDAVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYHAZDOMRSGM. You are receiving this because you commented.Message ID: @.***>
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— Reply to this email directly, view it on GitHubhttps://github.com/iBEAT-V2/iBEAT-V2.0-Docker/issues/5#issuecomment-2348891664, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A2KKO2JRPMVT52X42NG24CLZWLN55AVCNFSM6AAAAABN3SVH46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBYHA4TCNRWGQ. You are receiving this because you commented.Message ID: @.***>
ZZLXY
commented
2 months ago I deleted the image and pulled it again, and surprisingly, it worked stably on my server. I'm not sure why it was fixed, but in any case, thank you very much for the iBEAT team's continued support!
Hi, I ran the following command to process the T1w image:
docker run --gpus '"device=0"' --rm -v /home/ANAT/Data/batch01:/InfantData --user 1019:1017 ibeatgroup/ibeat_v2:release205 --t1 InfantData/Sub011-12.nii.gz --age 12 --out_dir result --sub_name Sub011-12 --skip_surface 0However, I encountered the following error: "Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map." Additionally, some files like '50175.mnc' were generated in the /home/ANAT/Data/batch01 folder. Does anyone know how to resolve this error? Thanks a lot!
Here’s the full output of the command:
iBEAT V2.0 pipeline processing
Pipeline input parameters: --t1 'InfantData/Sub011-12.nii.gz' --age '12' --out_dir 'result' --sub_name 'Sub011-12' --skip_surface '0' -- input age:12 T1w image: InfantData/Sub011-12.nii.gz No T2w image inputed! Model age in months: 12 Output folder: result/Sub011-12 Orientation code: T1w-ASR Doing reorientation and resampling... Original T1 resolution in RAI: 0.800000x0.800000x0.800000. New T1 resolution: 0.8x0.8x0.8 Original T1 size in RAI: 208x300x320. New T1 size: 208x300x320 Reorientation and resampling done! Doing N3 bias field correction... Use of uninitialized value $user in sprintf at blib/lib/MNI/MiscUtilities.pm (autosplit into blib/lib/auto/MNI/MiscUtilities/userstamp.al) line 167. [@513e7c43b3b9:/InfantData/] [2024-09-08 13:32:10] running: /usr/local/InfantPipeline/bin/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 100 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_1779/ 71699.mnc 91101.imp
Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Use of uninitialized value $user in sprintf at blib/lib/MNI/MiscUtilities.pm (autosplit into blib/lib/auto/MNI/MiscUtilities/userstamp.al) line 167. [@513e7c43b3b9:/InfantData/] [2024-09-08 13:46:24] running: /usr/local/InfantPipeline/bin/mni/bin/make_template -quiet -shrink 3 71699.mnc /var/tmp/nu_correct_1779//template.mnc
Smoothing volume: 96% done. (104/108) Time: 20 sec out of approx 20.7 sec Smoothing volume: DONE in 20 sec Use of uninitialized value $user in sprintf at blib/lib/MNI/MiscUtilities.pm (autosplit into blib/lib/auto/MNI/MiscUtilities/userstamp.al) line 167. [@513e7c43b3b9:/InfantData/] [2024-09-08 14:36:42] running: /usr/local/InfantPipeline/bin/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 100 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_2241/ 69367.mnc 3495.imp
Outputting Volume: ............................................................ Smoothing volume: 100% done. (81/81) Time: 25 sec out of approx 25 sec Smoothing volume: DONE in 25 sec Outputting Volume: ............................................................ Outputting Volume: ............................................................ Smoothing volume: 100% done. (81/81) Time: 20 sec out of approx 20.7 sec Smoothing volume: DONE in 20 sec Smoothing volume: ............................................................. Outputting Volume: ............................................................ Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Use of uninitialized value $user in sprintf at blib/lib/MNI/MiscUtilities.pm (autosplit into blib/lib/auto/MNI/MiscUtilities/userstamp.al) line 167. [@513e7c43b3b9:/InfantData/] [2024-09-08 14:51:53] running: /usr/local/InfantPipeline/bin/mni/bin/make_template -quiet -shrink 3 69367.mnc /var/tmp/nu_correct_2241//template.mnc
Smoothing volume: 99% done. (107/108) Time: 20 sec out of approx 20.3 sec Smoothing volume: DONE in 20 sec Use of uninitialized value $user in sprintf at blib/lib/MNI/MiscUtilities.pm (autosplit into blib/lib/auto/MNI/MiscUtilities/userstamp.al) line 167. [@513e7c43b3b9:/InfantData/] [2024-09-08 15:38:31] running: /usr/local/InfantPipeline/bin/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 100 -quiet -execute -clobber -nokeeptmp -tmpdir /var/tmp/nu_correct_2631/ 50175.mnc 59441.imp
Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Smoothing volume: ............................................................. Use of uninitialized value $user in sprintf at blib/lib/MNI/MiscUtilities.pm (autosplit into blib/lib/auto/MNI/MiscUtilities/userstamp.al) line 167. [@513e7c43b3b9:/InfantData/] [2024-09-08 15:54:07] running: /usr/local/InfantPipeline/bin/mni/bin/make_template -quiet -shrink 3 50175.mnc /var/tmp/nu_correct_2631//template.mnc
Smoothing volume: 100% done. (108/108) Time: 20 sec out of approx 20 sec Smoothing volume: DONE in 20 sec N3 bias field correction done! Doing skull striping... /usr/local/InfantPipeline/bin/Skullstripping_LiModel.py:38: SyntaxWarning: assertion is always true, perhaps remove parentheses? assert(dSeg[i]<=dFA[i], 'The output patch size should be smalled than input patch size!') WARNING: Logging before InitGoogleLogging() is written to STDERR W0908 16:30:13.262758 4169 _caffe.cpp:122] DEPRECATION WARNING - deprecated use of Python interface W0908 16:30:13.262784 4169 _caffe.cpp:123] Use this instead (with the named "weights" parameter): W0908 16:30:13.262786 4169 _caffe.cpp:125] Net('/usr/local/InfantPipeline/bin/LiModule/Skullstripping_T1_downsampled.prototxt', 1, weights='/usr/local/InfantPipeline/bin/LiModule/Skullstripping_T1_downsampled.caffemodel') W0908 16:30:13.264581 4169 upgrade_proto.cpp:71] Note that future Caffe releases will only support input layers and not input fields. In image: result/Sub011-12/T1-rescaled-RO-RS-n4-odd-downsample-hist-z200.nii.gz Out image: result/Sub011-12/T1-rescaled-RO-RS-n4-odd-downsample-hist-z200-skullpm.nii.gz Model path: /usr/local/InfantPipeline/bin/LiModule/Skullstripping_T1_downsampled.caffemodel Network structure path: /usr/local/InfantPipeline/bin/LiModule/Skullstripping_T1_downsampled.prototxt ('Input patch size: ', [64, 64, 64]) ('Output patch size: ', [64, 64, 64]) ('Step size: ', [12, 12, 12]) Error!!! Brain volume equals to 0. This is not normal! Please check the skull stripping probability map