Hi, I'm running QAtools on a set of subjects processed with FS 5.3.0, and consistently get this message when recon_checker is running:
Processing each subcortical label ... (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error etc. *And in the recon_check file I notice several of my subjects have this error message:* ERROR: Recon-all steps missing in subject <SUBJ_ID> status file Expected to see the following step(s): #@# Remove Neck ti. 22. mars 15:02:33 +0100 2016 in the recon-all-status.log file before (line # 12): --> CA Reg Inv *I ran recon-all -all, and the recon-all log file seems to indicate neck removal was peformed*; from recon-all.log: mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... -- writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 51 seconds. #-------------------------------------- #@# SkullLTA ti. 22. mars 14:45:17 +0100 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /cluster/software/VERSIONS/freesurfer-5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 -- reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... Apart from this, the snapshots look ok (except for one subject I asked about in a previous e-mail) and there are no outliers in any of the subjects (according to QAtools). Any idea why I get this error message? Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital 7006 Trondheim, Norway
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