Dear FreeSurfer group/Dr. Reuter,

My questions are in regards to the LONG stream.

My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

1) Error message
During the creation of the BASE, I get the following error in the beginning of the recon:
>>>WARNING: Image geometries differ across time, maybe due to aquisition changes?
         This can potentially bias a longitudinal study! Will continue in 10s.<<<<
What should I be aware of in regards to this error?

The images were all acquired using the same MPRAGE protocol.
All timepoints were fed MPRAGEs reconstructed in the axial orientation, but some may have been reconstructed at an angle. I was assured that this is not an issue for FreeSurfer, but could this be the reason for the error?


2) Conversion of LONG run aseg.mgz segmentations to native anatomical space

Executing the commands for converting aseg.mgz to native space MailScanner has detected a possible fraud attempt from "freesurfer.net" claiming to be (http://freesurfer.net/fswiki/FsAnat-to-NativeAnat) in the folder of a long run (me1.long.me_base) does not convert.

It seems to me that (unlike the cross runs) the long runs are all in the same space (in the template/ base space?) and their rawavg.mgz does not match that of the corresponding cross run. Some insight on this would be appreciated.

The question is how to convert an individual long run's aseg.mgz into native anatomical space. Perhaps using the rawavg.mgz from the corresponding cross run?

Thank you very much!
Ivan