Re: [Freesurfer] Robust PET signal projection

External Email - Use Caution Thanks Douglas. Is there a way to compute a weighted average in one command with fscalc ? Best, Matthieu Le mar. 18 déc. 2018 à 18:03, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> a écrit : > you can use mri_vol2surf to sample at different

Re: [Freesurfer] [PETsurfer] Use of MGX and RBV partial volume correction

External Email - Use Caution Hi Douglas, Thanks for these clarifications. I have however one misunderstanding. When sampling PVC corrected PET image onto surface: - I use bbpet2anat.lta when MGX was used as specified un tutorial - I use rbv2anat.lta when RBV was used But why

Re: [Freesurfer] [PETSurfer] Intensity normalization of PET images without PVE correction

External Email - Use Caution Hi Douglas, Thanks for helping. To have an only rescaled voxel-wise PET image, these options seem to work only when -rbv method is used and not -mgx. Do you know why ? Best, Matthieu Le mar. 18 déc. 2018 à 17:58, Greve, Douglas N.,Ph.D. <

[Freesurfer] Error while saving NPC results

External Email - Use Caution Dear Drs. Winkler, Greve, Fischl, et al. Could you help me understand which palm options are needed in order to produce tfce and clustere NPC results that are fwe-corrected across contrasts (i.e., _cfwep_)? I'm analyzing area and thickness and have

Re: [Freesurfer] mris_fwhm problem

No, not in the current framework. Even if there were, fwhm=.66 would not give you much smoothing. The intervertex distance is about 1mm, at fwhm=.66mm, the nearest vertex would be about 3 standard deviations away, meaning that the smoothing would be minimal. On 12/21/18 12:12 PM,

Re: [Freesurfer] recalculate mean cortical thickness and/or regional thickness using a SD threshold or exclusion mask

Hi Lindsay it might be easiest to do what you want in matlab. We do supply m-files for i/o of our various formats cheers Bruce On Thu, 20 Dec 2018, lindsay hanford wrote: External Email - Use Caution Hello Freesurfer Community,  I am wondering if it is possible to

Re: [Freesurfer] recon-all error : Too many intersected faces for face 120047

did you try to load it as a surface? If you want to upload the entire subject dir (tarred and gzipped) to our ftp site we will take a look. In the meantime you can also just post an image of the volume in 3 planes, that might help cheers Bruce On Fri, 21 Dec 2018, 허정선 wrote: External

Re: [Freesurfer] mris_fwhm problem

So, is there anyway around this issue? > > The smoothing works through iterative nearest neighbor smoothing, so the > fwhm is essentially discretized because you can't have fractions of an > iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1 > iteration, so it chooses 0. > > On

Re: [Freesurfer] mris_fwhm problem

The smoothing works through iterative nearest neighbor smoothing, so the fwhm is essentially discretized because you can't have fractions of an iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1 iteration, so it chooses 0. On 12/21/18 11:23 AM, sha...@nmr.mgh.harvard.edu

Re: [Freesurfer] surfreg cannot allocate memory

That’s odd – seems like somehow the file got corrupted. I suggest just regenerating the brain.mgz by running: mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz from your subject’s mri directory. That should fix things. best Andrew From: on behalf of Haoran

[Freesurfer] Postdoctoral position at UCL

External Email - Use Caution Apologies for the cross-posting and wide distribution. Postdoc advertisement == The NMR Research Unit is a multidisciplinary research team focusing on multiple sclerosis (MS). A Research Fellow is sought to work primarily on the

[Freesurfer] mris_fwhm problem

Dear Surfers, I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data (voxel size 1 mm iso)using the below command: mris_fwhm --s --hemi rh --smooth-only --i fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask

[Freesurfer] Freesurfer from source library dependencies dead link

External Email - Use Caution Hi Freesurfer folks! I am attempting to build freesurfer from source for our HPC center here at Brown University, but are running into a snag. Looks like the documentation points to a dead link for Step 3 of the freesurfer_linux_developers_page