Hi Martin,

Thanks for the information. I have another question which I just noticed:

so if all my individual data were processed and edited in the v 5.0, will it be problematic if I run the -base and -long in the v5.3 ? I noticed that in the tutorial, there was a line about:

Important Note! If you are re-processing existing longitudinal data processed by v5.0 or v4.5, and you are using v5.1 or newer, be sure to add the -clean flag to your recon-all string, as you will want to overwrite the brainmask.mgz and other files, since the base and long subject space is in a different space than in pre v5.1 runs. This is true for the -long stage as well.

So does that means I need to add -clean for the subjects I run - base -long in v5.3?

Also, if some of my subjects are running -base -long in the v5.0 ,and some are running in the v5.3, will it be problematic when I incorporate them in the post-processing stream?

Or should I just update my v5.0 to v5.3 and start running my -base -long in v5.3 using the data that was processed in the v5.0?

Thanks in advance,

Catherine

From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
To: Rongxiang Tang <rongxiangtang@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, September 3, 2013 2:00 PM
Subject: Re: [Freesurfer] questions regarding longitudinal processing

Hi Catherine,

running them with the normal recon-all command is the first step of the longitudinal pipeline, then create the 'base' (subject template) for each subject and finally run all individual time points again through the -long command.

see
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

for the description,

Best, Martin

On 09/02/2013 10:51 PM, Rongxiang Tang wrote:

Hi All,

This may seem to be an easy question, I would just like to confirm...

I have two groups that underwent different types of training and were measured at two time points (before and after training).

My understanding is that I should use the longitudinal scheme in freesurfer to run recon-all?

I have processed all data using normal recon-all command, and was wondering if I should rerun them all with the longitudinal command:
recon-all -subjid <tpNid> -all

Thanks in advance,
Catherine
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Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
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