Re: [Freesurfer] Cannot find subject for recon-all

External Email - Use Caution Thank you very much! It seemed to work but now it gives me another error message Pedros-Air:test1 pedrobarradas$ recon-all -i $SUBJECTS_DIR/test1/01.nii -s $SUBJECTS_DIR/test1 -all ERROR: You are trying to re-run an existing subject with (possibly)

[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] Cannot find subject for recon-all

External Email - Use Caution The message suggested subdirectory 'test1' already exists in your $SUBJECTS_DIR. Pass a different subjid to -s <>, or delete directory 'test1'. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Pedro henrique barradas Sent: Fr

Re: [Freesurfer] [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 Yau wrote: External Email - Use Caution Dear FreeSurfer expoerts,

[Freesurfer] Password

External Email - Use Caution I am attempting to use FreeSurfer on Windows via VirtualBox following this tutorial: https://secure-web.cisco.com/1ik6MYIt6QvMqWyWtidH8UaI3oL73sZCnfUSNQq80weZWAMGVpkPu6bFqAMA5EdVLKSo3nlgdPLQ718QxJfiRlNrvYq1MHmKf_FWFd-MaSgcUY5axZCE83CscGWAh4OWO-XPLMxKxo

[Freesurfer] recon-all for GM quantification

External Email - Use Caution Good afternoon, My name is Sofia and I work with Drs. Eva Ratai and Lilly Mujica-Parodi on the DCC project. I am reaching out to ask for your advice on a FreeSurfer question. I am using recon-all to try to quantify and compare GM volume and mean thi

Re: [Freesurfer] recon-all for GM quantification

External Email - Use Caution Hi Sofia Unfortunately that doesn't really work as the most time-intensive steps are required. We are working on replacing some of these with deep-learning equivalents, but it will be some months before that is available. Sorry Bruce From: freesurf

[Freesurfer] password

External Email - Use Caution Sorry, I have a problem. I am using FS_7_2_0_ubuntu_18_04_06.ova.7z on my virtual machine system but it wants a password to open it. What's the password of this file? Thank's ___ Freesurfer mailing list Freesu

Re: [Freesurfer] EasyReg Troubleshoot - Killed

External Email - Use Caution Dear Nadia, It seems like many centroids are missing. Did you visually check the segmentations of the reference and floating image, e.g., with Freeview? Do they look good? Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1b2Y7tMk