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If any more information is needed to address my question, please do let me know. I hope to hear back and once again thanks a lot for any assistance with this. Best wishes, Tudor On 1 June 2018 at 16:07, Tudor Popescu <tud...@gmail.com> wrote: > 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 > <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#LongitudinalProcessing51.LongitudinalStream.28recon-all-long.29>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 > >
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