[Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password

External Email - Use Caution Dear Freesurfer team, Could you provide me the password for the user 'developer' of the VM Freesurfer installation? Many thanks in advance, Best regards, Lester Melie-Garcia, PhDDepartment of Biomedical EngineeringUniversity of Basel. Switzerland.

Re: [Freesurfer] matlab: command not found - How can I solve this?

External Email - Use Caution Hello Camila, Did you try using the script fs_install_mcr, e.g., in the linux 7.2.0 release as freesurfer/7.2.0/bin/fs_install_mcr to install Matlab R2014b ?   Please note that there is a currently an issue with running it on M1 Macs. - R. On Oct 1,

Re: [Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password

External Email - Use Caution Sending the info to your private email shortly. - R. On Oct 1, 2021, at 14:51, Lester Melie-Garcia wrote:External Email - Use CautionDear Freesurfer team,Could you provide me the password for the user 'develo

[Freesurfer] Comparing volumes before and after editing

External Email - Use Caution Hello all, I'm very new to Freesurfer and have started with quality-checking recons. I wanted to know if there is a way to compare volumes before and after edits were made before recon-all has been re-run. For example, if we have brainmask.mgz tha

[Freesurfer] matlab: command not found - How can I solve this?

External Email - Use Caution Hey, I'm totally new into Freesurfer and I need some help with my Matlab. I tried to do "recon-all -s <.>/ -lgi But as you can see, It shows an error related to matlab... I tried everything! But nothing is working. I have heard that we should modify

Re: [Freesurfer] Not seeing effects of manual edits and re-running recon-all

The first thing to do is to re-run you data using different subject names so that you have an unedited version. You can then use mri_diff, eg, mri_diff unedited/mri/wm.mgz edited/mri/wm.mgz to determine if there is a differenece that you are just not seeing On 9/27/2021 7:16 PM, Kevin Miller wro

Re: [Freesurfer] Control for eTIV on Voxelwise Wholebrain Analysis?

Yes. Alternatively, if you are using mris_preproc, you can add --etiv to the command line and it will do the correction by dividing by the eTIV (rather than using a regressor). On 9/27/2021 2:51 PM, Wakim, Kathryn-Mary wrote: External Email - Use Caution Hi all, I'm currently runni

Re: [Freesurfer] What does Freesurfer do with a T2 if you do not use the t2pial flag

same thing On 10/1/2021 11:42 AM, Aaron Tanenbaum wrote: External Email - Use Caution What about for 7.1? On Fri, Oct 1, 2021 at 10:23 AM Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: What version are you running? In 7.2, it will automatically set the t2pial flag

Re: [Freesurfer] What does Freesurfer do with a T2 if you do not use the t2pial flag

External Email - Use Caution What about for 7.1? On Fri, Oct 1, 2021 at 10:23 AM Douglas N. Greve wrote: > What version are you running? In 7.2, it will automatically set the t2pial > flag when you specify -t2 > > On 9/27/2021 11:53 AM, Aaron Tanenbaum wrote: > > Externa

Re: [Freesurfer] What does Freesurfer do with a T2 if you do not use the t2pial flag

What version are you running? In 7.2, it will automatically set the t2pial flag when you specify -t2 On 9/27/2021 11:53 AM, Aaron Tanenbaum wrote: External Email - Use Caution What does Freesurfer do with a T2 if you do not use the t2pial flag? ___

Re: [Freesurfer] Freesurfer version

The 7.0.0 release was recalled because the intensity normalization *sometimes* did the wrong thing. It would not surprise me if you were not seeing any of these effects, but I can't guarantee that it won't happen in your data. If it was happening, you would see some big differences in the thick

Re: [Freesurfer] Color LUT after coregister and reslice aparc/aseg.nii

How did you reslice? If you used trilinear interpolation, then that would mess up the values; use nearest neighbor. Also, check out PETsurfer https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer which can do this sort of thing in a principled way On 9/27/2021 11:17 AM, Ryan Wales wrote:

[Freesurfer] FreeSurfer 7.1.0 VirtualBox Installation password

External Email - Use Caution Dear Freesurfer team, Could you provide me the password for the user 'developer' of the VM Freesurfer installation? Many thanks in advance, Best regards, Lester Melie-Garcia, PhD ___ Freesurfer mailing list