[Freesurfer] white matter measurements for labels/annotations

External Email - Use Caution Hi, is it possible to extract white matter volume estimations for labels/annotations? I am specifically wondering about the brodmann atlas and the stanford atlas that is already included in latest FS. Thanks, Victor Zeng Beth Israel Deaconess

[Freesurfer] Recon-all reconstructed image coordinates

External Email - Use Caution Dear Freesurfer developers, In the link below, you see two brains belonging to the same subject:

Re: [Freesurfer] TRACULA Question

External Email - Use Caution Hello, I just wanted to follow-up on my last message. I will be thankful if you can respond at the earliest time of your convince. Thanks and all the best, Ela From: Salar Dini, Elaheh Sent: Wednesday, January 26,

[Freesurfer] PETSurfer: error: MatrixReadTxT: could not scan value [1][1]

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to analyze amyloid PET data using PETSurfer. I am trying to do kinetic modeling and I am on the MRTM1 step. I have tried this two ways (one using the wiki instructions and the other using the tutorial

[Freesurfer] impact of defacing on eICV calculations

External Email - Use Caution Hi All, I have inherited some T1 data that are defaced. If I run the defaced images through freesurfer, will that impact the eICV calculations ? Please let me know. Many thanks Ri ___ Freesurfer mailing

[Freesurfer] Display PCC in cluster

External Email - Use Caution Hi, Douglas, I performed a group analysis and, after permutation, one cluster survived. How can I display this cluster over an inflated surface, but with colors representing the partial correlation coefficient? In other words, I would like to see the

[Freesurfer] Co-Registration after recon-all

External Email - Use CautionHi,   I ran recon-all on a MPRAGE-file, which was registered in freesurfer-space. Now I want to register other sequences like T2 in the same space using the registration matrix. What is the best way to do this? In bbregister I didn't found an option

Re: [Freesurfer] mri_normalize error MP2RAGE

External Email - Use Caution Dear Falk, thanks for the hint! My understanding was that the "robust" MP2 actually reintroduces some of the field inhomogeneity artefacts that MP2RAGE is designed to compensate (OBrien Plos One 2014) - that's why I am trying to go with

Re: [Freesurfer] mri_normalize error MP2RAGE

External Email - Use Caution Hi Cornelius, this doesn't address your issue directly and I may have simply been lucky, however, I haven't had any difficulties to process (7T) MP2RAGE data after background removal suggested by Marques et al.

[Freesurfer] mri_normalize error MP2RAGE

External Email - Use Caution Dear freesurfer experts,   when running recon-all (FS version 7.2.0) on skullstripped 3T MP2RAGE sequences, about 10-20% of scans from one scanner fail because of this:   mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz

[Freesurfer] Survey testing experimental setup

External Email - Use Caution Dear Freesurfer community, Have you ever wondered what is the impact that the experimental setup might have on reported results in neuroscience and psychology? If yes, you are not alone! We have created a survey to better understand and identify