Dear mailing list,
I am trying to batch a series of 30 MRI images using the following command: recon-all -autorecon2-cp -subjid ID001 -qcache
But for each image the process exits with the following errors: --------------------------------------------------- #@# 1/1 ID_001 Wed Aug 16 11:39:12 AEST 2017 -------------- ----------------------- mri_surf2surf --srcsubject ID_001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18138/ID_001.1.mgh --sval /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume --jac --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = ID_001 srcval = /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.18138/ID_001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.sphere.reg Loading source data Reading curvature file /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume ERROR: number of vertices in /mridata/workingdata/CHD/BAR/PROCESSING/baseline_5.3.fix/ID_001/surf/lh.volume does not match surface (109952,110385) ERROR: reading curvature file Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ID_001 exited with ERRORS at Wed Aug 16 11:39:13 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I came across an earlier post in relation to a similar error (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.h... https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-February/009807.html) where it was recommended that you run “recon-all -s subjid -make all” to rebuild all files where the dependency chain is wrong. I ran this for each of the subjects and then tried to rerun my original recon-all command again but got the same error. Do you have any alternate suggestions for fixing this problem?
Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
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