[Freesurfer] Could not login in "https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN"

External Email - Use Caution Hi teams, I could not login in "Could not login in "https://mail.nmr.mgh.harvard.edu/NMRAuth/GLOBAL/LOGIN"";. Thanks. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.e

[Freesurfer] aparc a2009s stats ROI names don't match ColorLUT for FS 6.0

External Email - Use Caution I have recently started using FreeSurfer 6.0 after previously working with 5.3 for several years. I found that the lh.aparc.a2009s.stats files use different ROI names (e.g., G&S_frontomargin) than they did in FS5.3 (G_and_S_frontomargin). However, th

Re: [Freesurfer] Tracula Inquiry

External Email - Use Caution Hi Jason, Tracula depends on FSL. If you have FSL installed, all that should be needed is to define FSL_DIR before sourcing `$FREESURFER_HOME/SetUpFreeSurfer.sh` So using your example above, you could go ``` export FREESURFER_HOME=/Applications/free

[Freesurfer] PetSurfer reference region

External Email - Use Caution Hello PetSurfer experts, We are using the cerebellum cortex as our reference region, but noticed that the SUVR values for lh/rh cerebellum cortex do not have a value of 1 (which is what we were expecting). The actual SUVR values are 1.31 for the lh a

Re: [Freesurfer] freesurfer- recon-all "exited with ERRORS"

External Email - Use Caution Dear Tim, Is it the FOV of my T1 image will affect the process Recon-all? If yes, how would it impact my output results? Regards Frank From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tim Schäfer

[Freesurfer] Tracula Inquiry

External Email - Use Caution Hello, I am having trouble carrying out Tracula on Freesurfer. See the following script (for confidentiality, patient's name has been replaced by XXX): Admins-iMac:~ neurology$ export FREESURFER_HOME=/Applications/freesurfer Admins-iMac:~ neurolog

[Freesurfer] Converting ANTs nonlinear transform to .m3z

External Email - Use Caution Dear FreeSurfer experts, I am working on some monkey data and trying to get an accurate nonlinear transform to talairach space (talairach.m3z in the -careg stage). The problem is that the monkey brains look so different from the human brain that this

[Freesurfer] recon-all with errors

External Email - Use Caution Dear Freesurfer experts, After running the recon-all in one of my subjets, part of the temporal lobe was partially excluded. Then, I tried to use the watershed algorithm to be less agressive in the skull stripping as follows: recon-all -skullstrip -ws

Re: [Freesurfer] 8 Gb of ram

I don't think our memory requirements change dramatically on a per-subject basis. The one exception might be topology fixing, but if it requires that much ram there are probably to many (or too large) defects to succeed in any case. cheers Bruce On Thu, 5 Mar 2020, Ian wrote: Exte

[Freesurfer] 8 Gb of ram

External Email - Use Caution Hey guys. I'm running Freesurfer on an AWS EC2 instance, in a docker container (t3.large specifically.) Would you expect 8Gb of ram to *always* be enough to run recon-all on a 280x280x240 T1 image? The instance is running Ubuntu; the container im

Re: [Freesurfer] ubuntu: run freesurfer in two terminal

External Email - Use Caution For 2 subjects that is what you can do. If you have a lot more, I would suggest to have a look at GNU Parallel [1]. It's also available in the Ubuntu package system. Best, Tim [1] https://www.gnu.org/software/parallel/ > On March 5, 2020 at 1:54

Re: [Freesurfer] mri_vol2surf produces invalid surface

External Email - Use Caution Thanks a lot. Now I understand what was wrong and resolve it. Shuntaro 2020年2月29日(土) 6:20 Douglas N. Greve : > > mri_vol2surf does not actually produce a surface, it produces a surface > overlay (ie, a value for each vertex). You can to run recon-all