Re: [Freesurfer] FSL not installed in setup

External Email - Use Caution FSL is not included in the freesurfer distribution and is covered by its own license, i.e. for release 6, FMRIB Software Library, Release 6.0 (c) 2018, The University of Oxford.  It can be downloaded and installed from their wiki page, https://sec

[Freesurfer] Volume transformation issue

External Email - Use Caution Hi, I am trying to transform a volumetric ROI from MNI152 space to native space. I am doing this in 2 steps. First (1) I am creating a registration file using bb register to create a registration file and then (2) I am using mri_vol2vol to transform vo

Re: [Freesurfer] Uncaught exceptions when processing some images with MiDeFace

External Email - Use Caution Patrick, I notice that you are running this on Frontera at TACC. I believe that TACC uses the Intel compilers as their default. I would guess that FreeSurfer is compiled with GCC, not Intel. You might try unloading the Intel compilers and loading th

[Freesurfer] FSL not installed in setup

External Email - Use Caution Hi Freesurfers, I am trying to run tracula and was running the command bedpostx_datacheck and the terminal said: freesurfer-darwin-macOS-7.3.2-20220804-6354275 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HO

Re: [Freesurfer] MiDeFace

External Email - Use Caution Hi Douglas, It is not going outward enough. I've attached the log file. Thanks for your help! Best, Jacob C Hermann Clinical Research Coordinator | Clark Neuropsychology & Neuroimaging Lab Department of Neurology | Icahn School of Medicine at Moun

Re: [Freesurfer] MiDeFace

External Email - Use Caution The algorithm works by projecting the average face inward and outward. In which direction is the problem occurring? Can you send me the log file? On 5/18/2023 12:16 PM, Hermann, Jacob wrote: External Email - Use Caution We have successfull

Re: [Freesurfer] Help Needed with Thalamic NucleiDTI Module and Freeview Display

External Email - Use Caution Hi, Thank you for your interest in our tool. Currently these three nuclei are not segmented by the network implementation, but they will be segmented by the Bayesian tool once we have integrated it into FreeSurfer. The Pc, VM and Pt are the three sm

[Freesurfer] MiDeFace

External Email - Use Caution We have successfully run MiDeFace on our neuroimaging files and it seems like a great option for our purposes (user friendly, easy to implement). However, we have noticed that there are some facial features (nose and mouth) that do not get obstructed

[Freesurfer] Help Needed with Thalamic NucleiDTI Module and Freeview Display

External Email - Use Caution Dear FreeSurfer Experts, I hope you are doing well. I have encountered an issue while using the Thalamic NucleiDTI module in FreeSurfer and would appreciate your guidance. I am attempting to segment the thalamus using the module, but the Pc, VM, and P

[Freesurfer] Password to uncompress VM freesurfer

External Email - Use Caution Hi, As per instructions I'm requesting the password to uncompress the freesurfer VM. Thanks. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees