New subject: adding time points to longitudinal base template

20 Oct 2014

      Hi Koushik,
no, I cc the list, maybe someone has done tests or seen papers. I read 
somewhere on atlas construction, that 10 images are fine, but that is 
cross subject. Here we only have small changes within subject, so from 
my experience less are fine , BUT
- 2 of course are not enough: in 2 the method is actually different (as 
the median in 2 is simply the average) . Starting with 3 a median 
intensity even exists for each voxel.
- adding 1 new to 5 existing may work without sacrificing too much bias, 
but adding 10 to 5 is not a good idea. Also if the one that is added is 
very different from the first 5 (e.g. first 5 within a week, next 3 
years later), then that will be problematic also.
Best, Martin
On 10/20/2014 12:07 PM, Govindarajan, Koushik Athreya wrote:
...
Hi Martin,
How are you? We had this below email conversation in March about 

the longitudinal template and it's stability. You had mentioned that 
with 5 time points, my template should be stable enough to patch 
another timepoint. I have another study that has only 2 time points 
and I was reading through your 2012 Longitudinal analysis paper that 
had used 2 time points to compare with cross-sectional data. I was 
wondering if you had any suggested literature for the number of time 
points needed for stability of a template.
Thanks
Koushik Govindarajan
*From:*Martin Reuter [mailto:mreuter@nmr.mgh.harvard.edu]
*Sent:* Friday, March 14, 2014 9:31 AM
*To:* Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] adding time points to longitudinal base 
template
Hi Koushik,
there is a way to add time points without recreating the base:
  recon-all -long <tpNsubjid> <longbasesubjid> -addtp -all
This is what the recon-all help says about that:
"If a new timepoint needs to be added to a longitudinal run where a 
base subject
has already been created (from prior timepoints), then the -addtp command
can be added to the -long command in order to 'fix-up' the longitudinal
stream to accept the new timepoint. Note that the base subject is *not*
recomputed using the new timepoint. This potentially introduces a 
bias, and it
is recommended to NOT add a time point this way! Instead recreate the base
from all time points and run all longitudinals again."
So it's up to you. But given you already have 5 time points in your 
base and add only 1, you may be fine. The base should be pretty stable 
with 5 and if the 6th is not too different, it should not matter much. 
I don't think anyone has ever done a thorough analysis about adding 
time points.
Best, Martin
On 03/11/2014 10:08 AM, Govindarajan, Koushik Athreya wrote:
Dear FS experts,

           I have a serial study in which I have run
cross-sectional and longitudinal analysis on 5 time points. Now, I
want to add a 6^th time point to my dataset. Do I have to rerun my
base template creation step from scratch or is there a way to just
add further time points to an existing template?

Thanks

Koushik

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Re: [Freesurfer] adding time points to longitudinal base template