Re: [Freesurfer] Question regarding recon-all

Hi Dan

yes, we typically use -i and read in the dicoms directly, but you can do it for a nifti also. Or you could create the 001.mgz and not use it, but there is no reason to (it's just more work).

cheers Bruce

On Thu, 8 Mar 2018, Levitas, Daniel wrote:

Hello,

I am running recon-all for the first time, and I am wondering when it is proper to use the -i option. My current recon-all command includes the -i option: recon-all -i T1.nii.gz -s 1020 -all, where T1.nii.gz is a nifti file of all 160 anatomical dicoms. I've seen some commands like this however: recon-all -s subjid -all​.  My question is, is it safer to specify the input, and if I choose not to, do I need to create an mri/orig/001.mgz file from mri_convert?

Thank you for the help,

Dan