Re: [Freesurfer] trouble converting between .mgz and .nii.gz

mri_info will give you the voxel-to-RAS matrix and the number of cols, rows, slices. I don't think those commands are doing what you think. I don't understand where vol2surf or cor2label come in. On 4/1/19 12:55 PM, JD Knotts wrote: > > External Email - Use Caution > > Hi Dr. Greve, > >

Re: [Freesurfer] trouble converting between .mgz and .nii.gz

External Email - Use Caution Hi Dr. Greve, Thanks very much for your reply! The lh.atlas.mgz file is a volumetric atlas (Kastner atlas ) generated for an individual subject as described here

Re: [Freesurfer] trouble converting between .mgz and .nii.gz

Not sure what is going on here. What is lh.atlas.mgz? Is is a surface overlay? What is subject_t1.nii.gz? If it is not the same geometry of lh.atlas.mgz, then strange things will happen when you do it a second time. On 3/31/2019 12:28 PM, JD Knotts wrote: External Email - Use Caution H

[Freesurfer] trouble converting between .mgz and .nii.gz

External Email - Use Caution Hello experts, As a sanity check in a pipeline I'm running I tried converting an atlas file containing visual ROIs from .mgz to .nii.gz and then immediately converting the resulting .nii.gz file back to .mgz: mri_convert lh.atlas.mgz lh.atlas.nii.gz -