[Freesurfer] (no subject)

External Email - Use Caution Hello All, I was wondering if the Right/Left-Cerebral-White-Matter in the aparc+aseg.mgz contains WM hypointensities. mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats --ctab FreeSurferColorLUT.txt Best, Paul

Re: [Freesurfer] eTIV and FSGD file

External Email - Use Caution Hello, I sent the message below a couple of weeks ago but I haven't seen it posted in my freesurfer digest emails. I am wondering if I need to do something different? It's the first time I submit something. Thanks, Juan From: Gallego Angel, Juan S

[Freesurfer] InfantFS witg segfile exiting with errors

External Email - Use Caution Dear FreeSurfer experts, I am trying to process some newborn subjects including the segfile. In both situations, including the mask file and using the --forceskullstrip flag I get the following error (log file attached): *lta_convert successful./hom

Re: [Freesurfer] bias field correction and intensity normalization

External Email - Use Caution Hi Matt, We always really appreciate your help and advice. Thank you very much for your answer, now we understand much better why it is correct not to apply this correction. Best, Marina ___ Freesurfer mai

Re: [Freesurfer] External 3D View Issue

I'm glad to hear it worked out Cheers Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Harriet Cornwell Sent: Tuesday, June 22, 2021 6:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] External 3D View Issue External Email - Use Ca

Re: [Freesurfer] Alveus voxels in the hippocampus

Dear Victor, We model the alveus in the atlas but don’t write it in the final segmentation because it’s unreliable and tends to leak out (mostly because of partial voluming, which messes up parameter estimation and segmentation). If you have small holes in the CA1 region over bright pixels, the

[Freesurfer] External 3D View Issue

External Email - Use Caution Hi Bruce, Thank you for your helpful suggestion - re-running it seems to have fixed the issue. Harriet Cornwell -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of freesurfer-requ...@nmr.mgh.harvard.edu Sent: 19 J

[Freesurfer] Alveus voxels in the hippocampus

?Hi, Sometimes I see empty space inside the CA1 in the FS7 hippo parcellations. These are voxels of bright intensities. Is this where the alveus is supposed to be labelled and are these brain scans that we should still be using for hippo? Victor Zeng Beth Israel Deaconess Medical Center Kes

[Freesurfer] Open PhD position - University of Oslo / Norway

External Email - Use Caution Applications are invited for a 3-4 year PhD fellowship available at the Department of Psychology, University of Oslo, Norway. All details about the position and a link to the application form can be found here: https://secure-web.cisco.com/1M7SwYGwD7y

Re: [Freesurfer] bias field correction and intensity normalization

External Email - Use Caution I respond somewhat with trepidation given that you did not take my advice previously; however, in case anyone else is wondering—I would not do this. In the absence of head motion, the T1w/T2w ratio will exactly cancel the receive field and will atte

[Freesurfer] bias field correction and intensity normalization

External Email - Use Caution Dear experts, I would like to create myelin maps calculating the T1w/T2w ratio. Should I apply bias field correction and intensity normalization (i.e., "nu correction" in the Freesurfer pipeline) to T1w and T2w images separately before calculating the