[Freesurfer] MacOS high Sierra, freesurfer development versiyon build problem! tar.gz

External Email - Use Caution Hi, I use freesurfer v6.0. im download freesurfer-darwin-OSX-ElCapitan-dev.tar.gz version but i could not build. I need codes to install the new version, how open tar.gz files? thanks for help. ___

Re: [Freesurfer] Troubles to determine the type of recon editing needed

Hi Matthieu the aseg is used to automatically edit the wm.mgz, which helps the creation of cortical surfaces. For example, the ventricles are filled using the aseg. I think in your case with greatly expanded ventricles, some of the ventricular voxels were incorrectly labeled in the aseg and

Re: [Freesurfer] Troubles to determine the type of recon editing needed

Hi Matthieu, The initial estimate for surfaces is based off the wm.mgz. Since you're wm.mgz is incorrect (due to the large ventricles and wm abnormalities) the first pass at a surface reconstruction is way off. The wm.mgz is created in-part from the aseg.mgz, so it is important that you

Re: [Freesurfer] Troubles to determine the type of recon editing needed

External Email - Use Caution Dear Bram, Thank you for your answer. As soon as possible I will run recon-all with the -bigventricles flag. Concerning the manual editing I don't understand well the aim of editing aseg.mgz since it seems to most concern subcortical structures and

Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files

Thank you very much for this! On Fri, Sep 14, 2018 at 2:53 PM, Hoopes, Andrew wrote: > Hi Lauren, > > > > You can find the new write_patch.m function here - > https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_patch.m > > > > You can install it with: > > > > curl

Re: [Freesurfer] fsaverage6 ?h.cortex.flat.patch files

Hi Lauren, You can find the new write_patch.m function here - https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_patch.m You can install it with: curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/matlab/write_patch.m > write_patch.m cp write_patch.m

[Freesurfer] Research Coordinator Job, Chicago, IL

External Email - Use Caution Research Study Coordinator job available at Northwestern University’s Mesulam Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL. Job Summary: Research Study Coordinator coordinates collection, analysis, processing & reporting of

Re: [Freesurfer] Troubles to determine the type of recon editing needed

If you haven't already, you may want to run the subject through recon-all with the -bigventricles flag since it looks like the lateral ventricle was significantly mislabeled in the aseg. If using the -bigventricles flag doesn't fix your problem, you can edit the aseg.mgz manually by following

[Freesurfer] Troubles to determine the type of recon editing needed

Hi Matthieu, I've taken a look through the files you shared with us and I see the poor surfaces in the posterior right hemisphere you were referring to in your message. It looks like your subject has a combination of abnormally large ventricles and significant wm abnormalities, so I'm

[Freesurfer] T2pial correction options

External Email - Use Caution Hi Freesurfer team, We’re having some trouble with the T2pial option. We are currently getting the Martinos Center ABCD project Tisdall/van der Kouwe vNav MPRAGE and T2SPACE at 0.8mm^3, bandwidth matched for distortion. Linked below are 2 gifs were