Re: [Freesurfer] [FreeSurfer] recon-all exited with error - watershed error

dly advise? Thank you so much. It's been grateful to have your guidance and support. Sincerely, Krystal FreeSurfer Version: 7.3.2 OS: Linux on Ubuntu 23.04 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Krystal Xiwing Yau Sent: 29 April 2

Re: [Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz

e about it? I'm using FreeSurfer 7.3.2 on Linux (OS Name: Ubuntu 23.04). Thanks a lot! Yours faithfully, Krystal From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Krystal Xiwing Yau Sent: 14 September 2023 17:14:12 To: freesurfer@nmr.mgh.harv

[Freesurfer] [FreeSurfer] regeneration of aseg.stats from manually edited aseg.mgz

External Email - Use Caution Dear FreeSurfer experts, I edited some images that under-segmented the brain by coloring the missing brain regions. When I used the edited aseg.mgz to regenerate aseg.stats, the new statistics did not show the increase of the volumes that I edited.

[Freesurfer] [FreeSurfer] ValueError axes don't match array

External Email - Use Caution Dear FreeSurfer experts, I have completed the processes of coregistration of FLAIR to T1 image for the subject. As I ran samseg with lesion contrast, the following error message occurred: writing template transform to /home/admin1/freesurfer/subj

Re: [Freesurfer] [FreeSurfer] recon fix the surfaces of the brain

can take a look? Cheers Bruce On Aug 2, 2023, at 10:24 PM, Krystal Xiwing Yau wrote: External Email - Use Caution Dear Bruce, Thank you very much for your advice. I am concerned about the large area of the brain not being segmented. The wm intensity ranged from 0 to 110, it goes

Re: [Freesurfer] [FreeSurfer] Process terminated when talairach was running

urfer] [FreeSurfer] Process terminated when talairach was running External Email - Use Caution That's weird. In the echo below, is that from your shell or on the HCP? When you source the FS environment, that variable will be set. On 5/12/2023 5:33 AM, Krystal Xiwing

[Freesurfer] [FreeSurfer] Process terminated when talairach was running

External Email - Use Caution Dear FreeSurfer expoerts, I am running recon-all for the subject on a HPC. It exited with error when talairach was running - it indicated "MINC_BIN_DIR: Undefined variable". The log file is attached to this email. I tried to look up the directory,

Re: [Freesurfer] [FreeSurfer] Error: mri_ca_register with non-zero status 143

, Your recon-all.log shows 'Command terminated by signal 15'. This indicates the system had delivered a SIGTERM to your recon-all process. Can you run it again? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Krystal Xiwing Yau Sent: Thursday, April 13, 2023

Re: [Freesurfer] [FreeSurfer] Error: mri_ca_register with non-zero status 143

rfer-boun...@nmr.mgh.harvard.edu > on behalf of Krystal Xiwing Yau > > Sent: Thursday, April 13, 2023 3:02 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] [FreeSurfer] Error: mri_ca_register with non-zero > status 143 > > External Email - Use Caution &g

Re: [Freesurfer] [FreeSurfer] recon-all exited with error

: Freesurfer support list Subject: Re: [Freesurfer] [FreeSurfer] recon-all exited with error Hi Krystal, Can you try running recon-all without ‘-parallel’ flag? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Krystal Xiwing Yau Sent: Saturday, February 18, 2023 7:45 PM To