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

External Email - Use Caution Dear Yujing, I will be using a different computer and run it again. Thank you! Best, Krystal From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: 22 February 2023 23:35:57 To:

Re: [Freesurfer] different clusters in mri_surfcluster output versus viewing in Freeview

This is actually a very obscure feature of freesurfer that takes some explaining. In FS, all p-values are computed with a two-sided test (so the sig.mgh represents a signed p-value). When you pass --sign pos to mri_surfcluster, it sees that you want to do a signed test instead of an unsigned

[Freesurfer] Tracula 6.0 - : Command not found. set: Variable name must begin with a letter. does not exist.DIR

External Email - Use Caution Hi Freesurfer Experts, I’m attempting to run Tracula and receiving the same error for both Tracula 6.0. Note: I have also tried updating to Freesurfer 7.2 and running recon-all (which runs without issue) and then Tracula (which returns the same

Re: [Freesurfer] Freesurfer Digest, Vol 228, Issue 26

mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Smith, Christine Sent: Tuesday, February 21, 2023 6:01 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] different clusters in mri_surfcluster output versus

Re: [Freesurfer] Infant Freesurfer - manual edits

External Email - Use Caution Dear all, Could anyone provide an update as to whether there is a way to incorporate manual edits into the infant Freesurfer pipeline? Thank you, Jee Won -Original Message- -- Date: Thu, 16 Feb 2023 13:38:44

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

Hi Amir, The reason that I asked about 7.2.0 is because the other user reported similar issue and they could run 7.2.0 recon-all without errors. I’m wondering if you could share your T1 and T2 images with us to further debug the issue? Best, Yujing From: AmirHussein Abdolalizadeh Sent:

Re: [Freesurfer] mri_robust_register --minsize

Hi Sebastien I believe that Doug has had success using bbregister for this. You might give it a try Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Reuter, Martin,Ph.D. Sent: Thursday, February 23, 2023 4:19 AM To: Freesurfer support list Subject: Re: [Freesurfer]

Re: [Freesurfer] Freesurfer Digest, Vol 228, Issue 26

External Email - Use Caution Thanks, that's perfect. Mark Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email:

Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

External Email - Use Caution Hi, I saw this thread and was wondering about the details of this patch. Does this patch affect the standard recon-all call or is this meant for a special flag. Also I was also wondering what issue did it solve? Thank you. On Wed, Feb 22, 2023 at

Re: [Freesurfer] mri_robust_register --minsize

Hi Sebastien, Robust register cannot register a slice into a 3D volume. It can only register 3d to 3d (or 2d to 2d, although that has not been tested much). Sorry, Martin On 30. Jan 2023, at 21:09, Proulx, Jean Sebastien wrote: Hello, I am trying to register a full volume to a single