[Freesurfer] BRAIN Initiative postdoc position available at LCN (FreeSurfer team)

Dear all, The Laboratory for Computational Neuroimaging (LCN) is seeking to fill a postdoctoral position in image analysis as part of an exciting NIH project titled: “Open-source software for multi-scale mapping of the human brain”, awarded to Drs. J. Eugenio Iglesias and Bruce Fischl as part o

[Freesurfer] dura edits .mgz~ file?

External Email - Use Caution Hello Freesurfers, I edited the brainmask.mgz file after running recon-all but no changes were saved. Instead I have a mysterious 'brainmask.mgz~' file that I cannot open with freeview. What is this file and does it contain my edits? If so how do I

[Freesurfer] Permutation simulation cluster include vertices below cluster-forming threshold

External Email - Use Caution Hello Freesurfers, I am using mri_glmfit-sim to find significant clusters using permutation simulation. My command is as follows: mri_glmfit-sim \ --glmdir lh.cn_ad.glmdir \ --perm 1000 3.0 pos \ --cwp 0.05 \ --2spaces \ --bg 1 When I open

[Freesurfer] mri_glmfit masking strategy

Hello Freesurfers, I need to perform a GLM in 25 patients versus 19 controls but I need the comparison to be done only on normal appearing cortex (in patients), thus excluding cortical lesions. * Is it possible to concatenate binary masks projected to surface? What command shall I use? *

Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

External Email - Use Caution Please find the logfile attached. Thank you Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve < dgr...@mgh.harvard.edu>: > Can you send the log file? > > On 6/4/2020 9:12 AM, Boris Rauchmann wrote: > > External Email - Use Caution >

Re: [Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

Can you send the log file? On 6/4/2020 9:12 AM, Boris Rauchmann wrote: External Email - Use Caution Dear FS experts, In my dataset I have 4 subjects where the T1 was acquired, planning the FOV very close to the occipital lobe. I guess that triggers the error: getSignalBehindHead ERR

[Freesurfer] gtmseg getSignalBehindHead ERROR (no slices behind head)

External Email - Use Caution Dear FS experts, In my dataset I have 4 subjects where the T1 was acquired, planning the FOV very close to the occipital lobe. I guess that triggers the error: getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7 slices behind head! ER

Re: [Freesurfer] Thalamic nuclei segmentation

External Email - Use Caution Dear Doctor Greve, Thank you for your reply. I am trying to do what you advised me. For now, I have segmented thalamic nuclei in the left hemisphere, checked and corrected this segmentation and used MRI_binarize as advised. However, I don’t know w