[Freesurfer] unable to map surface to fsaverage4

External Email - Use Caution Hi, I'm following the process described in https://www.cloudneuro.org/ to predict age based on cortical thickness of an individual brain. I cannot map surface to the fsaverage4 template by the 2nd command: recon-all -s subject.id -qcache -target fsav

[Freesurfer] Cerebellar Cortex Reconstruction

External Email - Use CautionDear all,   I ran recon-all with my dataset and I am pretty satisfied with the cortical reconstruction of both hemispheres. Unfortnuately, there was no Cerebellar reconstrucion. Is there any way to also get a surface reconstruction of the cerebellum w

[Freesurfer] Interpolate one volume into raster coordinate system of a second volume

Hello, I apologize for asking such a basic question, but I can’t find the right tool to interpolate a NIFTI brain volume (or DICOMs) into the raster coordinates of a second volume. I simply want a naive interpolation into the second volume’s coordinate system without performing registration.

[Freesurfer] combine orthogonal stacks

External Email - Use Caution Dear Experts, I don't know if this is even possible, but I'm hoping you can help. I have 3 clinical T1 scans in NIFTI format: one has good resolution in the axial plane one has good resolution in the coronal plane one has good resolution in the sagitta

Re: [Freesurfer] Interpolate one volume into raster coordinate system of a second volume

Hi Jason you can use -rl ("reslice like"): mri_convert -rl vol2.mgz vol1.mgz vol1_like_vol2.mgz cheers Bruce On Sun, 3 Mar 2019, Stockmann, Jason wrote:   Hello,     I apologize for asking such a basic question, but I can’t find the right tool to interpolate a NIFTI brain volume (or