Re: [Freesurfer] glmfit-sim FWHM 34?

External Email - Use Caution Hi Doug, thanks for your answer! This particular case is surface area. I thought I was using the FWHM15 smoothed data from outputted by qcache. I have no idea why FS tries to call FWHM34 in the glmfit-sim step. Should I have specified somewhere else

[Freesurfer] lazy symbol binding errors

External Email - Use Caution Dear experts, I was running mri2mesh command and I got this error: mris_convert /Users/davidemomi/Desktop/DAVE/sim_fem/fs_subj60/surf/rh.white /Users/davidemomi/Desktop/DAVE/sim_fem/m2m_subj60/tmp/wm.rh.stl dyld: lazy symbol binding failed: Symbol not

[Freesurfer] Euler number as quantitative quality measure

External Email - Use Caution Hey Freesurfer Experts, I would like to use the Euler number as a quantitative quality measure of my reconstructed data as Rosen et al. (2017) recommend in their recently published paper. https://www.sciencedirect.com/science/article/pii/S10538119173

[Freesurfer] FreeSurfer - Lateral Ventricle Definition

External Email - Use Caution Dear FreeSurfer Experts, Can you confirm whether, the volume of the choroid plexus has automatically been added to the laterel ventricle volume or not. Thanks Theo ___ Theophilus Akudjedu BSc, MSc, PhD Candidate Ro

Re: [Freesurfer] lazy symbol binding errors

Hello David, Please try downloading the following archive, unzip it, and follow the instructions in the README to update the files that have the lazy symbol issue. https://drive.google.com/open?id=1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR -rob On Jul 12, 2018, at 4:48 AM, Davide Momi mailto:momi.davi

Re: [Freesurfer] lazy symbol binding errors

Hello David, Please try downloading the following archive, unzip it, and follow the instructions in the README to update the files that have the lazy symbol issue. https://drive.google.com/open?id=1w0vZyWTY0HrbcDiP1jWsmGl_GMUSh7tR -rob On Jul 12, 2018, at 4:48 AM, Davide Momi mailto:momi.davi

Re: [Freesurfer] make_average_subject error

Hi Xiaoyu how are you trying to create an average subject? It looks like you are running recon-all on something. Typically we use the script make_average_subject for this cheers Bruce On Wed, 11 Jul 2018, Wang, Xiaoyu wrote: External Email - Use Caution   Hello FreeSurf

Re: [Freesurfer] Euler number as quantitative quality measure

Hi Lea the Euler number is an integer, so it will never be 2.5. In fact, in our reconstructed surfaces it will always be exactly 2, except for the *nofix* surfaces, as we explicitly correct the topology of the surfaces (see the Automated Manifold Surgery paper if you are interested in the det

Re: [Freesurfer] FreeSurfer - Lateral Ventricle Definition

Hi Theo it depends which volume you mean. In the current version of FS if you look in the aseg.stats there should be a line of the form: # Measure VentricleChoroidVol, VentricleChoroidVol, Volume of ventricles and choroid plexus, 19365.00, mm^3 later on in the file we list the volumes o

Re: [Freesurfer] lazy symbol binding errors

External Email - Use Caution Dear Robert, Thanks for both your help and your prompt response I've followed the instruction and everything seems fine Thanks again Davide Momi --- PhD Candidate Unit of Behavioral Economics and Neuroeconomics Department of Neuroscience, Im

Re: [Freesurfer] Regenerate Qcache without Recon-ALL

glad to save you some stress :) Bruce On Wed, 11 Jul 2018, Mr. Tass wrote: External Email - Use Caution jesus almost panicked there haha cheers mate From: freesurfer-boun...@nm

Re: [Freesurfer] Cortical Thickness at Individual Vertices

Hi James you could use techniques that compare the whole distribution of thicknesses across subject populations. You could do a t-test or something non-parametric like a Kolmogorov-Smirnov or use permutation testing. I'll cc Tom Nichols so he can chime in with something more sophisticated or

Re: [Freesurfer] glmfit-sim FWHM 34?

External Email - Use Caution Hi Douglas, I try to use permutation but it takes forever. I never see the end. Do I have to update the freesurfer to use the permutation? As it was recommended in this year? Best, Ting > On Jul 3, 2018, at 11:07 AM, Douglas N. Greve wrote: > > A

Re: [Freesurfer] Cortical Thickness at Individual Vertices (fwd)

from Tom -- Forwarded message -- Date: Thu, 12 Jul 2018 16:51:31 +0100 From: Thomas Nichols To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical Thickness at Individual Vertices External Email - Use Caution Hi Bruce! Jame

Re: [Freesurfer] fthresh function in tksurfer

HI Srishti, Please download the latest build from here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng > On Jul 11, 2018, at 3:49 PM, srishti goel <23srishtig...@gmail.com > > wr

[Freesurfer] questions about Tracula and doeddy=1 or 0

Dear FreeSurfer experts, I am analyzing a dataset (Q-Ball) of subjects with TRACULA on FreeSurfer 6.0. b1=0, b2=3000 s/mm2 and diff directions = 90. Surprisingly the trac-all reconstruction with doeddy =1 was not as good as with doeddy = 0 on average on all the subjects, as in our dataset ther

[Freesurfer] Tenure track faculty position at UAB

External Email - Use Caution The UAB Department of Neurobiology is accepting applications for tenure-track faculty positions. Join an excellent and rapidly growing group of colleagues! This is an open-rank, open research topic search and will continue until the positions are f

[Freesurfer] Tenure track faculty position at UAB

External Email - Use Caution The UAB Department of Neurobiology is accepting applications for tenure-track faculty positions. Join an excellent and rapidly growing group of colleagues! This is an open-rank, open research topic search and will continue until the positions are f