[Freesurfer] Longitudinal processing in v6.0 using manual edits from v5.3.0

External Email - Use Caution Hello FreeSurfer experts, We have a large dataset (n=140) that is being processed through the longitudinal pipeline. We have already generated the cross-sectionals and conducted manual edits to the bases in v5.3.0. What is the latest stage (cross, b

Re: [Freesurfer] differing display colors for 2+ labels in tksurfer

External Email - Use Caution I should also add that I cannot create an annot file as then all share multiple vertices. Best Idil From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Yagmur Oz

[Freesurfer] differing display colors for 2+ labels in tksurfer

External Email - Use Caution Hello freesurfer experts, I am aiming to view 3 to 8 different labels on one flattened surface patch created&viewed in tksurfer. Even if I can manually select the color of first label, the next ones end up sharing the same color and I cannot seem to

Re: [Freesurfer] Recon-all exited with errors

thanks Rob Bruce On Tue, 19 Jun 2018, Dicamillo, Robert wrote: I followed up with Ryan off the list one this one yesterday, i.e., he tried one of the later dev builds which fixes those lib issues.  I think recon-all runs for him now w/o the lib errors, but he is getting a non-zero exit from so

Re: [Freesurfer] Recon-all exited with errors

I followed up with Ryan off the list one this one yesterday, i.e., he tried one of the later dev builds which fixes those lib issues. I think recon-all runs for him now w/o the lib errors, but he is getting a non-zero exit from something else. - rob On Jun 19, 2018, at 11:00 AM, Hoopes, Andrew

[Freesurfer] Postdoctoral Fellowship in Neurobiological Bases of Reading (MRI and DTI)

External Email - Use Caution Dear colleagues, POSTDOCTORAL FELLOWSHIP IN NEUROIMAGING (MRI and DTI) The LandiLab (PI: Nicole Landi, PhD https://landi.lab.uconn.edu/) at Haskins Laboratories https://haskinslabs.org/ (which is closely affiliated with Yale University and the Universi

Re: [Freesurfer] Recon-all exited with errors

Hi Ryan, this issue should be fixed in the freesurfer development version, but as a temporary fix to get things working in v6, I would suggest disabling SIP and rerunning: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/ best Andrew From: on behalf of Ryan

Re: [Freesurfer] Using T2 or Flair data to improve pial surfaces

External Email - Use Caution I did not. Can I re-run a batch of scans with the -qcache command or do I need to do it one by one? Heidi Lindroth BSN RN PhD Candidate| School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Pred

Re: [Freesurfer] Using T2 or Flair data to improve pial surfaces

Did you run recon-all with -qcache ? On 6/19/18 9:30 AM, Heidi Lindroth wrote: External Email - Use Caution Hi there, I have used T2/Flair images to improve the pial surface reconstruction, however, when I tried to analyze these data in QDEC, I was unable to load the files because

[Freesurfer] Using T2 or Flair data to improve pial surfaces

External Email - Use Caution Hi there, I have used T2/Flair images to improve the pial surface reconstruction, however, when I tried to analyze these data in QDEC, I was unable to load the files because the T1/T2 processed scans do not have the following file type: lh.thicknes