[Freesurfer] GPL license with exceptions

External Email - Use Caution Hi, everyone, I'm developing a package that reads in files generated by FreeSurfer in some situations. The code was initially designed to publish in GPL-3. However, I noticed in your license agreement incompatible with this license. After reading some

Re: [Freesurfer] Queries regarding installation of FreeSurfer software

External Email - Use Caution Hello Dharmendra, It looks like you are trying to move the “..license” file out of the Applications folder using "sudo mv"- but the password is not being accepted ? You will need to know the admin password to use the sudo command. What version of

[Freesurfer] -fill-ribbon command.

External Email - Use Caution Dear Freesurfer experts, Although this issue was raised in the archive, I could not find an answer. I want to create a 3d volume using an annot file. I run the following command. 'mri_label2vol --annot $SUBJECTS_DIR/' subj

Re: [Freesurfer] FS edits of subcortical parcels

External Email - Use Caution Thx Doug. I'll give it a shot. Get Outlook for Android From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, August 17, 2020 12:31:58 PM To:

Re: [Freesurfer] FS edits of subcortical parcels

Start with editing aseg.manedit.mgz; these changes will propagate into wm.mgz, so only edit wm.mgz if it is wrong after the edits. Replace the voxels labels with the correct ones. In V6 run recon-all -s subject -autorecon2 -nogcareg  -nocanorm -nocareg -autorecon3 I would suggest doing a test

Re: [Freesurfer] FS edits of subcortical parcels

External Email - Use Caution Thx Doug. I presume I can just make WM edits to the wm.mgz at periphery of the ventricle but how about caudate/lentiform edits (which I have never had to do) . Do I replace incorrect voxels with the correct aseg labels (i.e. R caudate label 50)

Re: [Freesurfer] FS edits of subcortical parcels

Copy aseg.auto.mgz to aseg.manedit.mgz, then edit aseg.manedit.mgz. If you are using v7, then you can run recon-all -s subject -autorecon2-samseg -autorecon3 On 8/13/2020 5:35 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution FS editing experts, I have a subject with

Re: [Freesurfer] surf2vol from annotation?

On 8/13/2020 10:15 AM, Ellen Ji wrote: External Email - Use Caution Thanks Douglas. recon-all was performed using FS V6. However, we have since upgraded to V7. Should I stick with what was originally used (mri_aparc2aseg)? I don't think it will make much of a difference, so do

[Freesurfer] fs7..1.1 and age range

External Email - Use Caution Is 7.1.1. still considered to be best used as a pipeline for subjects older than ~5yo? Have any parts of the infant pipeline been incorporated so that it be used for babies or subjects up to 2yo, or do we still need to run separate infant pipeline?

Re: [Freesurfer] mri_vol2vol

First, check the overall registration with tkregisterfv --mov lowb.nii.gz --reg register.lta On 8/14/2020 12:30 PM, 侠义江湖，醉笑人生 wrote: External Email - Use Caution Hi, freesurfer experts. I am running dt_recon and mri_vol2vol to obtain FA values of ROI. Everything is OK after running