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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
