Dear all,

I have pre and post-intervention data for a single group of subjects, and I'd like to extract the cortical thickness pre and post, for all standard regions in the atlas, and use those in subsequent analyses.

Following the standard approach for longitudinal studies, I used the following types of commands:

1. recon-all -i 01_1.nii.gz -subjid 01_1
   recon-all -i 01_2.nii.gz -subjid 01_2
   recon-all -i 02_1.nii.gz -subjid 02_1
   ..
   where e.g. 01 is the subj code, and _1 and _2 represent pre and post scans
2. recon-all -subjid 01_1 -all
   recon-all -subjid 01_2 -all
   ..
3. recon-all -base 01 -tp 01_1 -tp 01_2 -all
   ..
   
4. recon-all -long 01_1 01 -all
   recon-all -long 01_2 01 -all
   ..
   

However, the base step has led to warnings of the type: "WARNING: Image geometries differ across time, maybe due to aquisition changes?  This can potentially bias a longitudinal study! ", and consequently to an empty /stats folder -- even though my pre and post images are aligned and have similar acquisition parameters.

Have I done something wrong, and how can I fix this warning/error? Many thanks in advance for any help.

Best wishes,

Tudor