When you say they are growing rather than shrinking, do you mean in the longitudnial recon-all run? The reason I ask is that you only mention the base and cross. When you do the longitudinal analysis, you need to do cross, then base, then long.

On 6/15/2022 11:43 AM, Wittayer, Matthias wrote:

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Dear community,

I tried to process MS- patient’s MRIs (mostly same scanner, same settings) Longitudinally over a long period of time. I first processed all timeponits crosssectionally and then initialised the base image by recon- all – base TP1 TP2 TP3 etc. Now I am trying to run label based morphometry and it seems some areas are growing rather than shrinking. Which is highly unlikely. I tried to exclude timepoint of a relapse to rule out perifocal edema interfering with measures but the problem remains.

Did anybody have the same problem?

Is it a potential bug or just a garbage in garbage out problem (though I don’t know what would be wrong with our scans)?

Does it make sense to make an intermediate template for two timeponits only? I.e. recon- all –base TP1 TP2; recon –all –base TP2 TP3 … and use them for longitudinal runs?

Thanks for your opinions. Best

Matthias
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