[Freesurfer] NextBrain with 333 labels

External Email - Use Caution Dear FreeSurfer experts I tried to segment my brain MRI using NextBrain.in the most recent FreeSurfer-dev package. I followed the command in https://secure-web.cisco.com/150f92dNZNQHVJBK1fmC5Z4FYOqCYvgP1aIrq7dafQUxfyrR4wSHgPGLPwf0jxqrEBJqs-9YISyUo_u7_O

Re: [Freesurfer] Qt platform and lta_convert error

External Email - Use Caution  You may be missing packages on your system freesurfer needs to run if you did not install freesurfer with the .deb package installer   You can download the 7.4.1 Ubuntu 22 installer from,https://secure-web.cisco.com/1Tsk98POal2iEABYPOiUI6g759awF8BwG

Re: [Freesurfer] Freesurfer - skull stripping error

Thanks a lot for the advice!!. One thing that is still not clear to me: at which freesurfer step do you use synthstrip (or the manual version)? I am trying to run autorecon1 and then swap the brainmask but then autorecon2 fails. Best, Sara Inviato da Outlook per iOS _

Re: [Freesurfer] Freesurfer - skull stripping error

External Email - Use Caution I just want to add (from out of nowhere) that synthstrip is fantastic..highly reliable and accurate. Josh Lee Assistant Professional Researcher Department of Psychiatry and Behavioral Sciences University of California, MIND Institute jki...@ucda

Re: [Freesurfer] Freesurfer - skull stripping error

Synthstrip is extremely robust, it on both Cheers Bruce On Sep 29, 2024, at 6:34 PM, De Giorgi, Sara wrote:  Thank you all for the help. I have available the T1 post contrast, could I use it alternatively? (After freesurfer analysis I have to do tracula analysis). Thanks, Sara Inviato da Out

Re: [Freesurfer] Freesurfer - skull stripping error

Thank you all for the help. I have available the T1 post contrast, could I use it alternatively? (After freesurfer analysis I have to do tracula analysis). Thanks, Sara Inviato da Outlook per iOS Da: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] FreeSurfer - extract rigid parameters from .lta file

External Email - Use Caution Hello FreeSurfer Developers, I am using mri_robust_register to register a moving volume to a fixed one. The algorithm outputs the rigid transformation in a .lta file. I need to extract the rigid parameters (3 rotation angles in degrees and 3 translati

Re: [Freesurfer] Freesurfer - skull stripping error

You could try synthstrip, it might work Cheers Bruce On Sep 29, 2024, at 7:38 AM, William Baare wrote:  External Email - Use Caution Hi Sara, You need to denoise the background. Here are some links that might be of help. Always check the quality of the output :-) https://github.com