yes, exactly.
On Thu, 8 Mar 2018, Levitas, Daniel wrote:
Hi Bruce,
Thanks for your response. Just to clarify, I can run recon-all with the -i
option and not create the 001.mgz file from mri_convert because recon-all will
perform the conversion anyway?
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu>
Sent: Thursday, March 8, 2018 1:37 PM
To: Freesurfer support list
Subject: 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
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