Re: [Freesurfer] hippocampal subfield segmentation question

Dear Gabor, It’s all about the physical coordinates, so (b) is the right answer! /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Gabor Perlaki Reply-To: Freesurfer support list Date: Saturday, 11

Re: [Freesurfer] (no subject)

External Email - Use Caution Thanks, that solution seems to work finally. I just ignored the remaining voxels labeled according to the standard aseg scheme and proceeded with the the PET analysis and the combined LUT. I will ignore the remaining fragment labels from the original

Re: [Freesurfer] Edit surface in Freeview

External Email - Use Caution Thanks Doug, I followed your tips and try to run mris_remove_intersection. However the result looks like the same than before. Maybe I am doing something wrong. Could you please provide me more details? Do you have any other suggestions? Thanks

Re: [Freesurfer] Noise reduction + Eddy current reduction

External Email - Use Caution In general these days the more recent “eddy” tool is preferred for eddy current correction of diffusion data. Matt. From: on behalf of "Greve, Douglas N.,Ph.D." Reply-To: Freesurfer support list Date: Saturday, January 11, 2020 at 2:54 PM To:

Re: [Freesurfer] Noise reduction + Eddy current reduction

No, I've always used FSL's eddy_correct On 1/11/2020 2:17 AM, Adam Rytina wrote: External Email - Use Caution Hi Greve, thanks for your answer. I will try ANTS DenoiseImage. Regarding Eddy Current - moreover, i have to reduce the eddy current on DWI images. Does Freesurfer enable to

Re: [Freesurfer] Edit surface in Freeview

YOu can try running mris_remove_intersection (or something like that) On 1/11/2020 12:48 PM, Davide Momi wrote: External Email - Use Caution Dear Freesurfer expert, I am working with bem model and I have created the outer and the inner skull. Unfortunately, for few subjects the two

[Freesurfer] hippocampal subfield segmentation question

External Email - Use Caution We have a sagittal 1 mm isotropic whole-brain 3D T1 mprage (morphometry protocol suggested on Freesurfer's page) and a coronal anisotropic (0.4mm inplane, 2mm thickness, similar to ADNI protocol) T2 measurement acquired perpendicular to the

[Freesurfer] Edit surface in Freeview

External Email - Use Caution Dear Freesurfer expert, I am working with bem model and I have created the outer and the inner skull. Unfortunately, for few subjects the two surfaces intersect each other (see attached). I've tried to edit it manually but I had hard time in figuring

[Freesurfer] Extract specific LGI values

External Email - Use Caution Dear FreeSurfer Experts, I am Tien Pham, I am stucked at this situation. I calculated longitudinal LGI changes in my data set with two time points using longitudinal pipeline. Now I would like to extract the regional LGI and gray matter volume in my

Re: [Freesurfer] Noise reduction + Eddy current reduction

External Email - Use Caution Hi Greve, thanks for your answer. I will try ANTS DenoiseImage. Regarding Eddy Current - moreover, i have to reduce the eddy current on DWI images. Does Freesurfer enable to perform the eddy current reduction? Thanks a lot Regards Adam