External Email - Use Caution
Hi there, I was trying to extract the hippocampus parts of a T1 MRI dataset with 292 samples as it is mentioned in the documentation (" https://secure-web.cisco.com/1BAyhN9FdUHAAqUD8DOQTWc8CqCVlTa3xgiGxxFItgCG2AP..."). when I was trying to use the recon-all command, after almost 1 hour of processing I encountered this error: """ mri_watershed Error: GLOBAL region of the brain empty ! Command exited with non-zero status 1 """
I appreciate your time for helping me. Note that I attached the recon-all.log for your review if it is needed.
External Email - Use Caution
This happens in one case or in all 292? You should follow the processing stream backwards to see where things first went wrong. It could be the skull stripping, but it might also be one of the inputs to it is already incorrect like the T1.mgz or transforms/talairach_with_skull.lta
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Iman Kianian Sent: Saturday, August 26, 2023 9:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_watershed Error while running recon-all
External Email - Use Caution Hi there, I was trying to extract the hippocampus parts of a T1 MRI dataset with 292 samples as it is mentioned in the documentation ("MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1tcOiUdhh28Tixh--tJ08X0ReDV6gcct7x0LIeS8WLC4BHf...https://secure-web.cisco.com/1BAyhN9FdUHAAqUD8DOQTWc8CqCVlTa3xgiGxxFItgCG2APPd1nEg4nE3AptgHfWColMe_ee-GG4i4us5pFR-e51GoSTb-V91YTdzNaKaTHiJURDzVAskrDzx4-OL41nRZUIXRxfqHTkxl3kOkQb2inZvcnrdhZWsuK6fu9M6-qXDo0PWGQXHRdlqYGBZkmVOJRcvcYSbe7LF4csk6Tjxpmj7Tl22CupnIdxYan7VkqsamjxZ9-3RYG6V2L0RDgMDPozCB--6uRxrY8gMdoT4jna17JZGlTlOnWIPASOwKZgtiBZQuemvhtgaduiq0rSSgjX8K3ik5Cg0NzHwpx_QxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala"). when I was trying to use the recon-all command, after almost 1 hour of processing I encountered this error: """ mri_watershed Error: GLOBAL region of the brain empty ! Command exited with non-zero status 1 """
I appreciate your time for helping me. Note that I attached the recon-all.log for your review if it is needed.
External Email - Use Caution
I noticed all 292 images were processed in the same recon-all. I’m wondering if they are from the same subject.
If they are data from longitudinal study, you can process them with longitudinal pipeline - https://secure-web.cisco.com/1DWOFf8HXjewTlDOa5xZ86rZJrfN2Gj9YRwV79Y5tc02bjF...
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Iman Kianian Sent: Saturday, August 26, 2023 9:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_watershed Error while running recon-all
External Email - Use Caution Hi there, I was trying to extract the hippocampus parts of a T1 MRI dataset with 292 samples as it is mentioned in the documentation ("MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1nDPXI5J4jwZAl4biV-62p60LDxcYoL5HoOu8ciGeukr-da...https://secure-web.cisco.com/1BAyhN9FdUHAAqUD8DOQTWc8CqCVlTa3xgiGxxFItgCG2APPd1nEg4nE3AptgHfWColMe_ee-GG4i4us5pFR-e51GoSTb-V91YTdzNaKaTHiJURDzVAskrDzx4-OL41nRZUIXRxfqHTkxl3kOkQb2inZvcnrdhZWsuK6fu9M6-qXDo0PWGQXHRdlqYGBZkmVOJRcvcYSbe7LF4csk6Tjxpmj7Tl22CupnIdxYan7VkqsamjxZ9-3RYG6V2L0RDgMDPozCB--6uRxrY8gMdoT4jna17JZGlTlOnWIPASOwKZgtiBZQuemvhtgaduiq0rSSgjX8K3ik5Cg0NzHwpx_QxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala"). when I was trying to use the recon-all command, after almost 1 hour of processing I encountered this error: """ mri_watershed Error: GLOBAL region of the brain empty ! Command exited with non-zero status 1 """
I appreciate your time for helping me. Note that I attached the recon-all.log for your review if it is needed.
freesurfer@nmr.mgh.harvard.edu
-
Fischl, Bruce R.,PHD -
Huang, Yujing -
Iman Kianian