Hi Han,
there is two things going on here.
1. for some reasons there are small differences in the acquisition parameters
across your time points. This usually indicates that there was a change in
protocol wich could bias your longitudinal study (depending on what was changed
and if this is consistent across subjects or not).
2. It seems recon-all has a problem with this many time points. The shell is
bad at handling very long strings, I think it probably concatenates the
individual directory names somewhere and then get’s the word overflow. I cannot
fix that right now (and it may not even be that easy to fix at all). So I would
recommend to select a subset of your time points (like up to 10), create the
base and then add the remaining time points later to the existing base (there
is —addtp or similar to do that). When you select the 10 make sure they are
equally distributed across your 30 time points (beginning, middle, end of the
series).
Best, Martin
> On Aug 16, 2016, at 8:54 AM, Hanbyul Cho wrote:
>
> Dear FreeSurfer experts,
>
> I am FreeSurfer longitudinal processing the thirty time points data.
> When I tried the step 2 process to make a template, the process stopped with
> an error.
> The error message as the below.
>
> ===
> ...
> mri_diff --notallow-pix /home/Desktop/MyProject/CO30/mri/rawavg.mgz
> /home/Desktop/MyProject/CO30/mri/rawavg.mgz
>
> Volumes differ in geometry row=1 col=1 diff=0.054242 (0.054242)
>
> ***
> WARNING: Image geometries differ across time, maybe due to aquisition changes?
> This can potentially bias a longitudinal study! Will continue in 10s.
> ***
>
> Word too long.
>
>
> ==
>
> My command line was:
> recon-all -base SET1template -tp CO01 -tp CO02 ... -tp CO30 -all
>
> How can I fix the error?
>
> Best wishes,
>
> Han
>
>
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