[Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999

External Email - Use Caution Dear Freesurfer Experts,   I have few questions regarding CWP values from mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999.   Using the 3 three commands below (A, B and C):   A. mri_glmfit-sim  --glmdir lh_status.glmdir --perm 1 1.3 abs

Re: [Freesurfer] Fwd: Whole Thalamus Volume

They’re different modules with different algorithms, which give different yet very highly correlated results. So, whatever you use the volumes for further down the stream, the results should be very similar with either version. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow

Re: [Freesurfer] Extracting hierarchical hippocampal segmentation volumes

Hi Kelsey, The volumes are derived from the probabilistic segmentation at the finest level of detail, so there’s no direct mapping to the different hierarchical segmentations. Your safest bet is probably to count the number of voxels in the hard segmentation and multiply by the volume of the

Re: [Freesurfer] MEMPRAGE vs. MP2RAGE

Oh, sorry, yes I remember now. I guess mp2rage naturally sacrifices some SNR/unit time to get flatter images. I think Doug (and Jon, now included) can comment on this Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Caspar M. Schwiedrzik Sent: Monday, September 7, 2020

[Freesurfer] Results summary in QDEC

External Email - Use Caution Dear Freesurfer experts, I performed group analysis in QDEC in order to compare cortical thickness between two groups using the Monte Carlo Z simulation correction. My question is, where is located the z-score of each significant cluster? Maybe in the

[Freesurfer] Fwd: Whole Thalamus Volume

External Email - Use Caution -- Forwarded message - From: Al Qadi, Ameen Date: Fri, Sep 4, 2020 at 6:09 PM Subject: Whole Thalamus Volume To: Freesurfer support list Dear Freesurfer Developers, I noticed a significant disparity in the left and right whole

Re: [Freesurfer] MEMPRAGE vs. MP2RAGE

External Email - Use Caution Hi Bruce, In that paper, you reported that MP2RAGE underestimates cortical thickness relative to MEMPRAGE and also has slightly lower reproducibility. Since Recon-all does not seem to have built in functionality to deal with the background noise in

Re: [Freesurfer] Freeview not starting on Ubuntu 16.04: "failed to initialize XRandr"

External Email - Use Caution Hi Thanks for the quit reply. I followed those instructions, it seemed that all those libraries were already installed. Freeview still won’t launch (even after rebooting). Here’s the output of the second command you suggested: alexlw@alexs:~$

Re: [Freesurfer] MEMPRAGE vs. MP2RAGE

Hi Caspar Can you elaborate? What are the issues? Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Caspar M. Schwiedrzik Sent: Monday, September 7, 2020 2:27 AM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] MEMPRAGE vs. MP2RAGE External Email - Use Caution

Re: [Freesurfer] Updating Freesurfer Version

External Email - Use Caution Hi Freesurfer experts, I’m trying to update my current Freesurfer version (from 6.0 to 7.1). I’d like to know whether the installation procedure for 7.1 would overwrite the current one (6.0). Many thanks, Pilar > Il giorno 22 ago 2020, alle ore

Re: [Freesurfer] Freeview not starting on Ubuntu 16.04: "failed to initialize XRandr"

External Email - Use Caution Hello Alex, I’m not sure Ubuntu 16.04 LTS has everything installed by default that the Qt graphics framework is looking to run in the X windows server. You could try installing, $ sudo apt-get update$ sudo apt-get install libx11-dev libxext-dev

[Freesurfer] MEMPRAGE vs. MP2RAGE

External Email - Use Caution Hi! I was wondering whether the issues with surface reconstruction from MP2RAGE data that were reported for Freesurfer v5.1 in Fujimoto et al., 2014 still persist in more recent releases of Freesurfer, and whether there is information to what extent