[Freesurfer] FS7.1 CentOS8 build-stamp.txt

External Email - Use Caution Hello everyone, I just wanted to point out that the build-stamp on the CentOS8 build of FS7.1 includes the text “centos7” which raises some questions among users as to which one we have installed. It’s a tiny detail, but I’m sending this message to

Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)

Dear Elizabeth, Please add the flag “-rt nearest” to prevent interpolation ;-) Also: some of the smaller labels may disappear in the resampling… Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Elizabeth Haris

Re: [Freesurfer] Longitudinal Stream Problem

If you run this, it will create a new brain.finalsurfs and rerun just what you need to rerun recon-all -s subject -autorecon2 -nogcareg -nocalabel -nonormalization2 -autorecon3 On 6/22/2020 1:20 PM, Danielian, Laura (NIH/NINDS) [E] wrote: External Email - Use Caution Interesting – I

[Freesurfer] Freesurfer 5.3.0 recon-all failure

External Email - Use Caution Hey guys. I have need to run recon-all from freesurfer 5.3.0.  When I do I get this error: INFO: SUBJECTS_DIR is /execute Actual FREESURFER_HOME /usr/local/freesurfer Linux ca9b4aef337a 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 14:58:26 UTC

Re: [Freesurfer] FS7.1 CentOS8 build-stamp.txt

Thanks Tyler, The centos8 download links to the centos7 build. It's a bit misleading, so we will probably change that. Best Andrew On 6/23/20, 4:24 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tyler Ward" wrote: External Email - Use Caution Hello eve

Re: [Freesurfer] Longitudinal Stream Problem

External Email - Use Caution OK thanks. Do you recommend that I re-run this for every subject that I did these cerebellar edits on since it ended up editing brain.finalsurfs.mgz? I have a handful of other data sets where it didn’t affect the longitudinal surfaces, but upon fur

Re: [Freesurfer] T1 stats output name confused

External Email - Use Caution Hi Douglas, So basically, aparc+aseg.stats are generated from aparc+aseg.mgz, which segment T1-weighted image into gray matter, white matter, ventricles, non-ventricular cerebrospinal fluid and lesion. Is that correct? Thank you ! Best, Qi On Mon, Ju

Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)

External Email - Use Caution Ah! Thank you, Eugenio 😊 (it fixed it slightly, so I’ll take it!) From: on behalf of "Iglesias Gonzalez, Juan E." Reply to: Freesurfer support list Date: Tuesday, 23 June 2020 at 11:29 pm To: Freesurfer support list Subject: Re: [Freesurfer] Runni