External Email - Use Caution Hi,
I am trying to use the longitudinal pipeline of the “hippocampal subfields and nuclei of amygdala”. Keep getting error messages when running it longitudinal but with no error message running it cross-sectional. I want to know if there is any way to fix the error and to run a longitudinal pipeline successfully. I am using Freesurfer/dev and matlab_runtime/2014b. I got two timepoints for each subject and finished recon-all longitudinal with no errors. 1) First Try segmentHA_T1_long.sh SUBJ_base >> run for about 15 mins and exited with error message: “Error using kvlGEMSMatlab /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMeshDeformationOptimizer.cxx:327: itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2ac1fead7740): search direction is not a descent direction! Error in kvlStepOptimizer (line 11) Error in SegmentSubfieldsT1Longitudinal” >> no mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 generated. 2) Second Try segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_base segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_base >> run for about 16 mins, most successful but a few with errors: “Error in segmentSubjectT1_autoEstimateAlveusML (line 1539)” Or >> “Open file failed because file '/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m' has invalid content. Details: 'file is closed.failbit is set.' The file "/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m" cannot be executed. Error in segmentSubjectT1_autoEstimateAlveusML (line 538)” >> successful done subject or hemisphere generated mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21. 3) Third Try cross-sectional segmentHA_T1.sh SUBJ1_timepoint1 segmentHA_T1.sh SUBJ1_timepoint2 >> run for about 15 mins, all successful with no errors: >> all subjects have mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 generated. Manual inspection with freeview, it seems fine with all successful longitudinal and cross sectional subfield segmentation outputs mgz. I wonder if I can fix first try and second try errors so that longitudinal output can be generated. Thank you for your help! Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai
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