Re: [Freesurfer] REPOST: Longitudinal Stream: Recon-all and template

Hi Tamara

1. Run each timepoint through the cross-sectional stream separately.

2. recon-all will figure out what files to use when you tell it to create the base.

cheers Bruce

On Thu, 30 Jun 2016, Tamara Tavares wrote:

Hello All,

I am planning to run the longitudinal stream on my data set and I have a few questions:

1. When I run the data cross sectionally using "recon-all -all" should I

specify all my subject's T1 volumes (using the -file1.nii -1file2.nii) or can I run each of my subject's T1 volumes individually through recon-all? My understanding is that some motion correction will occur if I specify more than one T1 which may alter the results versus if I specify one T1?

2. What input files should I use to create my base templates? Are the input

files the norm.mgz files from each subject?

Thank you in advance for your help!

Best, Tamara