Re: [Freesurfer] Question on using thalseg_1.1.h5

External Email - Use Caution Many thanks and apologies, Henry - I figured it out... I stupidly replaced your improved segmentation script in both the scripts and the bin directory instead of only replacing the former. many thanks for your time, much appreciated g

Re: [Freesurfer] Recon-all stuck at topology fix

Hi Salil This looks like a T2-weighted volume. Recon-all by default assumes T1 weighting. Do you have a T1 you can use (like an MPRAGE or FLASH scan)? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bhole, Salil Sent: Thursday, April 11, 2024 12:36 PM To: Freesurfer

Re: [Freesurfer] Surface vertex tkr-ras to native T1 RAS without volume files

These three TAGs (TAG_SURF_DATASPACE, TAG_SURF_MATRIXDATA, TAG_SURF_TRANSFORMEDSPACE) are available in the surface files if they are output from Freesurfer dev version. They are the same as the metadata DataSpace/MatrixData/TransformedSpace in GIFTI. You can use the information to convert [x,

[Freesurfer] Surface vertex tkr-ras to native T1 RAS without volume files

External Email - Use Caution Dear FreeSurfer devs, I'm writing a program in JavaScript that converts FreeSurfer surface (mesh) files to other formats, which require the vertices to sit in scanner RAS coordinates. Right now I'm relying on the FreeSurfer *brain.finalsurf.mgz* or

Re: [Freesurfer] surface-based filtering

Hi Jiaen I'm not sure what you mean by "stacked smoothing". I think the N in nsmooth is the number of iterations of nearest neighbor smoothing to apply, which converges to Gaussian as N gets bigger. Not sure about the units for fwhm - I defer to Doug on that Bruce From:

Re: [Freesurfer] surface-based filtering

External Email - Use Caution Hi Bruce Thanks for your response. In the help, I found the following options. Is the fwhm based on voxel unit? Does nsmooth-in or-out control the number of stacked smoothing? --fwhm-src fwhmsrc: smooth the source to fwhmsrc --fwhm-trg fwhmtrg:

[Freesurfer] surface-based filtering

External Email - Use Caution I'm wondering if freesurfer provides functions to filter the surface data within certain neighborhood exclusively on the surface. It's essentially similar to regular smoothing in 3D space. But the filtering kernel only runs on the surface. I can

Re: [Freesurfer] surface-based filtering

Yes, we support surface-based smoothing. Check out the help for mri_surf2surf Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Jiaen Liu Sent: Thursday, April 11, 2024 2:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] surface-based filtering

Re: [Freesurfer] surface-based filtering

External Email - Use Caution I thought N controls the number of smoothing iterations and the smoothing in each iteration is defined by fwhm which is some measurement of the smoothing kernel width. Can I ask how to achieve smoothing effect similar to gaussian smoothing with

Re: [Freesurfer] mri_synthmorph

Hi Antoine, I would guess this is a memory issue. You could try allocating more and/or look at the exit code. I believe 137 would indicate that Python ran out of memory. Malte From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Antoine Royer

[Freesurfer] BBRegistration with FSL topup

External Email - Use Caution Hi, I had a question as to how to integrate fsl's topup command for correcting B0 distortion with freesurfer's boundary-based registration. I am working with high-resolution epi data (0.8mm isotropic) with a reduced FOV and am trying to register it

Re: [Freesurfer] WMH-SynthSeg - Torch module not found

External Email - Use Caution The current nightly build dated April 12th available from

Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

External Email - Use Caution Hi experts, A follow-up question: how to verify if the results (gtm.stats.dat) generated by mri_gtmpvc make sense? Thanks, Angel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of WONG Wan Wa Sent: