Re: [Freesurfer] mri_synthseg on Mac M3

External Email - Use Caution If you downloaded the latest dev build from,https://secure-web.cisco.com/1rfGZf44C3EnYEUAAH8Ai3U46OACeadGiVwnMr-cmtNHSPnxGsIht2tUaKMvt5ObEWav9ChRQU7z92P60YOqKLC_gngOhS9K7saRX1GA0b_ie2vnIDMlAapl0jIkDHVeTLuOPKLNiBQHkNPxCamp-Byb_IrftUrJ9wNFBsjB2savuid_pKB

[Freesurfer] How to interpret the vertex-wise area metric?

External Email - Use Caution Dear FreeSurfer experts, I have a question about the interpretation of the vertex-wise area metric. For instance, if Vertex A had a larger area than Vertex B, then what's the difference between Vertex A and Vertex B biologically?  Based on my

Re: [Freesurfer] use and registration of FLAIR in recon-all and segmentHA (@Eugenio)

On 11/12/2024 6:58 AM, Simone Cauzzo wrote: External Email - Use Caution Hi all I am running Freesurfer 7.4 I use recon-all with the -FLAIRpial option. 1) I wonder whether the FLAIR to T1 registration is handled by recon-all or whether I need to supply a FLAIR image already registe

Re: [Freesurfer] Resampling FLAIR images with anisotropic voxels

Is this just a visualization issue? What is your freeview command? On 11/12/2024 3:55 AM, Koen Van Leemput wrote: External Email - Use Caution Hi Jin, To me it doesn't sound like a resolution issue: samseg will happily "eat" whatever resolution you have in your images, although for

Re: [Freesurfer] Appropriate image for texture/intensity based analysis

I would recommend the norm.mgz as it should be scaled so that the WM is 110 and bias fields would have been (mostly) removed. On 11/12/2024 12:06 AM, Sandhitsu Das wrote: External Email - Use Caution We want to perform appearance-based analysis that also takes advantage of automated

Re: [Freesurfer] mri_vol2surf error: GM estimation couldn't find enough samples

what is your command line? On 11/11/2024 3:47 PM, Lee, Hansol wrote: Dear FreeSurfer developers, I am attempting to use “mri_vol2surf” command to project output from diffusion MRI models (e.g., DTI) onto the cortical surface. The registration between the diffusion MRI and anatomical space

Re: [Freesurfer] mri_label2label

Can you take a look at your images and the aseg.presurf.mgz segmentation and the rh.orig.nofix? The program that is throwing an error is trying to determine where the non-cortical medial wall is based on the aseg and the orig.nofix. If one or both of those are bad, then it may fail. On 11/11/

Re: [Freesurfer] aparcstats2table & asegstats2table version differences

It is certainly fixed in 7x version. I think it is fixed in the patch per the documentation On 11/7/2024 3:41 PM, Heffernan, Zachary wrote: External Email - Use Caution Hello FreeSurfer Mailing List, I see in the Release Notes

Re: [Freesurfer] FS version 8-beta

I think this should work, though it might exit early due to the bug that I just posted. But a fixed version should be able to do this. On 11/7/2024 2:37 PM, Aaron Tanenbaum wrote: External Email - Use Caution Awesome, Will this version be able to process over older versions of FreeS

[Freesurfer] FS 8-beta bug report

FYI: I just found a bug where recon-all will exit with error the second time it is run. This will be fixed in the final release. doug ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfe

[Freesurfer] mri_synthseg on Mac M3

External Email - Use Caution Dear all, I have followed the instructions on the following thread to get synthseg and synthstrip working on a Mac M1 running Mac OS 14.4.1. https://secure-web.cisco.com/1z0NvcyulyAlPNPdO0aoX9HmzbTLQxZpEv8dVkKqSnsr7R1UzSrBWhhHzMEtaV1olEDAkP37CpNga2

[Freesurfer] Systematic difference in volume between baseline and longitudinal pipelines

External Email - Use Caution It seems the original posting did not go through likely because it had an attachment. Here it is again. I have seen some threads from a few years ago discussing differences in thickness, and we see this in volume as well (v6). I had an attached plot fo

[Freesurfer] use and registration of FLAIR in recon-all and segmentHA

External Email - Use Caution Hi all I am running Freesurfer 7.4 I use recon-all with the -FLAIRpial option. 1) I wonder whether the FLAIR to T1 registration is handled by recon-all or whether I need to supply a FLAIR image already registered to T1. 2) in case recon-all handles th

Re: [Freesurfer] Resampling FLAIR images with anisotropic voxels

External Email - Use Caution Hi Jin, To me it doesn't sound like a resolution issue: samseg will happily "eat" whatever resolution you have in your images, although for multicontrast data such as yours you'd need to resample all contrasts to the image grid of one contrast (typical