Re: [Freesurfer] Convert 1D mgh back to 3D

The mgh files look like surface overlays judging from their dimensions (163842 x 1). The values are for corresponding surface vertices. I'm not sure if Freesurfer already has a program to do the conversion. But I think you can do it with the following steps: 1. locate the surface file that the

[Freesurfer] dt_recon, CC_Anterior (T1) and FA corregistration.

External Email - Use Caution Hi: I used the following commands: dt_recon --i sub-OAS30003_ses-d1631_run-01_dwi.nii.gz --b sub-OAS30003_ses-d1631_run-01_dwi.bval sub-OAS30003_ses-d1631_run-01_dwi.bvec --s OAS30003_MR_d1631 --o dt_recon_result cd dt_recon_result mri_vol2vol --mo

Re: [Freesurfer] Issues with FS 7.3 skull stripping but NOT mri_synthstrip

Hi Carly, SynthStrip has been included since FreeSurfer 7.3 but not as the default skull-stripping method before the 8.0 beta release. You can explicitly enable it by adding the `-synthstrip` flag to your recon-all command and setting the environment variable FS_ALLOW_DEEP to 1. Details can be