Dear All,

I have run into problems with a longitudinal analysis using v5.0.0 (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) that seemed to work fine under v4.5.0. For both analyses I processed the raw data from scratch since they were run on different clusters.

Following the instructions at http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing I initially processed all images using the cross sectional stream, eg

  recon-all -s PATIENT016_TIMEPOINT1 -i PATIENT016_TIMEPOINT1

then created a template from all time points for each subject, eg

  recon-all -base PATIENT016 -tp PATIENT016_TIMEPOINT1 -tp PATIENT016_TIMEPOINT2 -tp PATIENT016_TIMEPOINT3 -all

Finally I tried to run the longitudinal processing stream, eg

  recon-all -long PATIENT016_TIMEPOINT1 PATIENT016 -all

where I ran into the following error message

“ERROR: longitudinal base ID cannot be the same as a timepoint subject ID (in /home/asimmons/images/FREESURFER/PATIENT016/base-tps)

Find more info at: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing”

The longitudinal base ID is however not the same as any of the timepoints in /home/asimmons/images/FREESURFER/LNDMCI016/base-tps which just contains a list of the time points as expected -

PATIENT016_TIMEPOINT1

PATIENT016_TIMEPOINT2

PATIENT016_TIMEPOINT3

Best wishes,

Andy Simmons

----

Dr Andy Simmons

Reader in Neuroimaging & Consultant Clinical Scientist

Centre for Neuroimaging Sciences and NIHR Biomedical Research Centre

Institute of Psychiatry, Box P089

Kings College London

De Crespigny Park

London, SE5 8AF, UK

Email - andy.simmons@kcl.ac.uk

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