Re: [Freesurfer] mri_label2vol with fill-ribbon option

Hi Junjie, Can you specify the Freesurfer version you are running? Thanks. Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Wu, Junjie Sent: Saturday, June 11, 2022 11:15 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_label2vol with fill-ribbon option

[Freesurfer] about the error on running TRACULA using tutorial data

External Email - Use Caution Hi I downloaded the FreeSurfer tutorial data ( https://secure-web.cisco.com/1tDso4rjIlURcoFeNGyGUBBs1I7uczKauIIt12c78g81fRPOWsCdQGwqpysQpOHQv0zCfd4ugm0Hc5rEJwBAoS2uuC6V3tPvJ7pPBrzpiXz-2lMVqq14rv-USdZ-PY38Ec-9wLMQE4FbcZWz7V0k95amZWvMPhp0vrbfxmtXJcHkn5M

[Freesurfer] Incorporating samseg segmentation into the recon-all pipeline

Hi Julian, You can use the command "samseg" with the --recon flag. See the helper function for more details (--help) Stefano External Email - Use Caution /Hello everyone,/ /We have been utilizing freesurfer for our brain morphometry and processing pipelines, and have recently tested the sa

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

Hi Ben, I was able to reproduce the core dump. In my case, it was because a mismatch of color scheme between input annotation file and the color table loaded with the surface. I suspect it might be the same issue for you too. But I’m not sure what the right action is to work around this. Yuj

Re: [Freesurfer] mris_preproc read error

External Email - Use Caution Dear FS team, There was indeed a problem with recon-all and I reran the subject and did what you said, and now there is no mris_preproc read error. Thank you very much for your assistance! All my best, Joanna -- Joanna Eckhardt Neurosciences Gra

[Freesurfer] recon-all -s exited with ERRORS

External Email - Use Caution Hi, FreeSurfer Developers, I am attempting to use the recon-all to reconstruction, I successfully run this command in some subjects, but it also failed in around 1/3 of subjects. And after running the recon-all of this 1/3 subjects. It will show “

[Freesurfer] using brain mask from older FreeSurfer version on a newer

External Email - Use Caution Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to do. I see that you can give freesurfer a brainmask. I was thinking of giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a wise idea? Do you have any obje

Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

External Email - Use Caution The problem is solved, I just changed the freesurfer version , thnx for your help Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum a écrit : > External Email - Use Caution > > Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of sc

Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

External Email - Use Caution Great. glad I was of some help. I still need my questions answered. On Tue, Jun 14, 2022 at 4:33 PM Bouchra Guelib < bouchra.gue...@univ-constantine2.dz> wrote: > External Email - Use Caution > > The problem is solved, I just changed the frees

Re: [Freesurfer] TRACULA -bedp parallel processing

External Email - Use Caution I tried to troubleshoot this, but I couldn't. I just want to follow-up and make sure no other solutions come to your mind. If not, we will run it out of cluster which seems to work just fine. Thanks and all the best, Ela _

[Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors

External Email - Use Caution Dear FS Help Team, I run FS on Ubuntu VM Virtualbox 6.1 on Windows. Out of nowhere, my Virtualbox is no longer opening and has errors. See screenshots below. First screen looks like this upon launching the Virtualbox and so I click Ubuntu and then it

Re: [Freesurfer] TRACULA -bedp parallel processing

Unfortunately it's not something we've been able to replicate here ? From: Salar Dini, Elaheh Sent: Tuesday, June 14, 2022 8:53 PM To: Yendiki, Anastasia ; Freesurfer support list Subject: Re: TRACULA -bedp parallel processing External Email - Use Cauti

Re: [Freesurfer] Ubuntu VM Error - /dev/sda1 contains a file system with errors

External Email - Use Caution If you boot into recovery mode, there is an fsck option available there you can try.   I will send some screenshots of booting into recovery mode to your email directly. - R. On Jun 14, 2022, at 21:06, Joanna L Eckhardt w