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 hanbyul.h.cho@gmail.com 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)

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WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s.

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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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