Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

2023-02-09 Thread fsbuild
External Email - Use Caution When you say you are running Mojave, I think you probably meant to write 10..14.6 (not 10.16.6). You could check you have the latest version of XQuartz (2.8.5) installed

[Freesurfer] Request for 7 zip password

2023-02-09 Thread Nathaniel Bailey
External Email - Use Caution Hello, I would like the passcode for the 7 zip file FS_7_2_0_Ubuntu_18_04_06.ova.7z so that I can install the Freesurfer virtual image. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] FS FAST

2023-02-09 Thread Justin Oh
External Email - Use Caution Hi Avnish, Justins-MacBook-Air:~ justinoh$ whereis python3 python3: /usr/bin/python3 Justins-MacBook-Air:~ justinoh$ which python Justins-MacBook-Air:~ justinoh$ which python3 /usr/local/bin/python3 Justins-MacBook-Air:~ justinoh$ brew info

Re: [Freesurfer] change labels name

2023-02-09 Thread Kumar, Avnish
Hi John, You can edit the label names in the accompanying metadata file of your Atlas - maybe a .txt or .lut file? You can edit that in a simple text editor. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of John Anderson Sent: Thursday, February 9,

Re: [Freesurfer] change labels name

2023-02-09 Thread Huang, Yujing
Hi John, I think you will have to load a different lookup table. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of John Anderson Sent: Thursday, February 9, 2023 9:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] change labels name External Email

Re: [Freesurfer] MRI image quality metrics

2023-02-09 Thread John Anderson
External Email - Use Caution You might consider the command wm-anat-snr to compute SNR On Thu, Feb 9, 2023 at 10:38 AM Kumar, Avnish wrote: > You could also use these: > >1. For CNR you can use the mri_cnr tool: > > mri_cnr [options] > > For example: > > mri_cnr

Re: [Freesurfer] MRI image quality metrics

2023-02-09 Thread Kumar, Avnish
You could also use these: 1. For CNR you can use the mri_cnr tool: mri_cnr [options]  For example: mri_cnr $SUBJECTS_DIR/bert/surf/ $SUBJECTS_DIR/bert/mri/norm.mgz 1. For SNR, you'll have to calculate them as: * Run the recon-all pipeline to process your MRI data. * Use

[Freesurfer] change labels name

2023-02-09 Thread John Anderson
External Email - Use Caution Dear Freesurfer, I have a volumetric atlas in nifti format. I can open this atlas in freeview. Using the Lookup Table>FreesurferColorLUT, I can see how every label has a specific color. When I move the mouse cursor over an area of this atlas. I can see

Re: [Freesurfer] FS FAST

2023-02-09 Thread Kumar, Avnish
Can you post the outputs of these three commands: which python which python3 brew info python Best, Avnish From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Justin Oh Sent: Tuesday, February 7, 2023 11:18 AM To: Freesurfer support list Subject: Re:

Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

2023-02-09 Thread Wang, Ruopeng
Can you try the latest dev build from here? https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Ruopeng On Feb 8, 2023, at 2:28 PM, Rankin McGugin mailto:rankin.mcgu...@gmail.com>> wrote: External Email - Use Caution of course, see attached Rankin W. McGugin, PhD Research

Re: [Freesurfer] T2pial: Numerical argument out of domain

2023-02-09 Thread AmirHussein Abdolalizadeh
External Email - Use Caution Hi Yujing, Trying with 7.3.0 also results in the same error. Of note, running recon-all 7.3.2 without -T2/FLAIR and -T2/FLAIRpial flags works without any issues. However, I couldn't try recon-all in the 7.2.0 version (I can give it a try if you think