Re: [Freesurfer] Pial and WM edits around the temporal lobes

Hi Stephanie can you show us an example of what you mean? And also give us details about what FreeSurfer version you are using and what data you are acquiring? cheers Bruce On Mon, 14 Jan 2019, Stephanie Otto wrote: External Email - Use Caution Greetings Freesurfer Team, W

Re: [Freesurfer] -qcache error

External Email - Use Caution I am new to FS, and I am having the same error that Krishna had last year. I don't see a link to the 'lh.white.k' file in my surf folder. Has anyone resolved this problem? I can side step the error with '-qcache -measure thickness' to only process t

[Freesurfer] Pial and WM edits around the temporal lobes

External Email - Use Caution Greetings Freesurfer Team, We are working on quality checking reconstructions and there seems to be a common problem area around the temporal lobes where the white matter surface extends beyond the pial surface, or the pial surface just looks off. We k

Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution Hi Doug Thank you very much for this. I am unfortunately not able to get the new version to work with our system. Is it possible to send a version built for centos6/rhel6? Thanks again! - James From: free

Re: [Freesurfer] Grey matter excluded from pial surface

Hi Inês it's tough to tell from a few images. I would guess it is a topological defect caused by a spotty segmentation. If you tar and gzip the entire subject dir and ftp it to us with the location of the problematic areas we will take a look cheers Bruce On Mon, 14 Jan 2019, Borges Pereira

Re: [Freesurfer] problem using recon-all

External Email - Use Caution thanks, hope it'll work anyway, looking forward for the version 6 release cheers, Shachar On Mon, 14 Jan 2019 at 14:08 Glasser, Matthew wrote: > Ubuntu 14.04 should still work. > > Matt. > > From: Shachar Gal > Date: Monday, January 14, 2019 at 5:4

[Freesurfer] Issues parcellating with a custom atlas

External Email - Use Caution Hello My interest is to create an aparc+aseg file with a combination of a cortical parcellation with a custom cortical atlas and the subcortical grey matter components from the standard asegbasically i want to mask and extract signal from multiple

Re: [Freesurfer] problem using recon-all

External Email - Use Caution Ubuntu 14.04 should still work. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Monday, January 14, 2019 at 5:43 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>>, Matt Glasser mailto:glass...@wustl.edu>>, Ido Tavor

Re: [Freesurfer] problem using recon-all

External Email - Use Caution if the problem is with the versions, maybe downgrading my OS for now will do the trick? do you happen know what is the latest ubuntu that is compatible with the 5.3-HCP version? does this also occur in centOS? thanks On Sun, 13 Jan 2019 at 17:46 Shach

Re: [Freesurfer] Problem with checking registration quality using tkregister-sess: if: Expression Syntax.

External Email - Use Caution Hi Everyone I've managed to fix my problem. In case anyone else has the same problem, the problem was that the subject name was repeated twice in the subjectname file within the subject_ID (in my case 20_1) folder. Best wishes, Keri On Thu, Jan 10, 2