Hi Catherine,
1. the -clean flag is only necessary if you used 5.0 or earlier for the full longitudinal stream. You only used it for the first step (the cross sectional processing). 2. yes, it's a bad idea to process different subjects with different version. It's OK to use 5.0 for cross and a newer version for base and long as long as you do it for all subjects the same way. So you need to do all -base and all -long with the same (best 5.3) version.
Best, Martin
On 09/04/2013 11:43 AM, Rongxiang Tang wrote:
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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