Re: [Freesurfer] Convert mgz to nii

Hi Jessica in general if you specify .nii or .nii.gz as the extension of any output file we will write it in nifti format. This makes using mri_convert easy: mri_convert any_volume.mgz any_volume.nii.gz should work fine cheers Bruce On Sun, 31 May 2020, Hua, Jessica wrote: Exte

Re: [Freesurfer] Convert mgz to nii

External Email - Use Caution Hi FreeSurfer experts, Also in case the code is different, how would I convert my T1.mgz file to a .nii file to be used in DTI analyses? Thanks! Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psycho

Re: [Freesurfer] Convert mgz to nii

mri_convert aparc+aseg.mgz aparc+aseg.nii.gz should do the trick cheers Bruce On Sun, 31 May 2020, Hua, Jessica wrote: External Email - Use Caution Hi FreeSurfer experts, I would like to convert my .mgz parcellation file to a .nii file to be used in DTI analyses.  How would

[Freesurfer] Convert mgz to nii

External Email - Use Caution Hi FreeSurfer experts, I would like to convert my .mgz parcellation file to a .nii file to be used in DTI analyses. How would I convert my participant's aparc+aseg.mgz file to a .nii file? Best, Jessica --- Jessica Hua, M.A. Cognitive and Emotio

Re: [Freesurfer] Running amygdala segmentation on a warped brain (fsaverage-to-MNI152)

External Email - Use Caution Hi Eugenio, Just to double check I understand: 1. If I run segmentHA_T1.sh on the output from recon-all, then the output from segmentHA_T1.sh is also in fsaverage space (not native space)? * If this is correct, then can I just warp this se