Dear all, I am facing problems in completing the longitudinal pipeline with recon-all.
Here is the detail: FS version (downloaded two weeks ago): freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 The longitudinal pipeline given in recon-all was exactly followed as: 1) cross-sectionally process tpN subjects (the default workflow): recon-all -s tp1 -i path_to_tp1_dicom -all recon-all -s tp2 -i path_to_tp2_dicom -all 2) create and process the unbiased base (subject template): recon-all -base longbase -tp tp1 -tp tp2 -all 3) longitudinally process tpN subjects: recon-all -long tp1 longbase -all recon-all -long tp2 longbase -all The first two steps (running recon-all for each tp individually and base template creation) went ok without errors. However, the third step tp1.long.base ended with errors and the recon-all.log file crashed during the mris_label2annot command: cmdline mris_label2annot --s tp1.long.base --hemi lh --ctab /home/shahidm/software/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading ...../surf/lh.orig 1 1530880 BA1 ERROR: lh.BA1.label, n=0, vertex 1711302004 out of range In other runs, the same command throws an error of Segmentation fault (core dumped). Could you please suggest how to investigate further the causes and solutions to this problem? Thanks a lot, Best regards, -- Shahid.
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