Hi Aura, 1. What do you mean by “loading Matlab 8.2”? It should be Matlab 8.4 (2014b). 2. “Some still did”: what error did you get?
- Also, I’m confused by what you wrote, that subfields worked but hippocampal module didn’t (aren’t they the same thing?) - Finally: can you please send us a screenshot of one of those abruptly cut hippocampi, so I better understand what might be going on? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Hurtado, Aura Maria" <ahurt...@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, 21 March 2018 at 22:24 To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal Subfields Module, output error Hi, I am attempting to use the longitudinal pipeline of the "hippocampal subfields and nuclei of amygdala”, but keep getting a flawed output. My dataset consists of images from a longitudinal study with some dropouts. First, I ran the reconall longitudinal pipeline in fs60 for all subjects. I got no errors. Then, I tried 1. Running the longitudinal pipeline of the hippocampal module, loading Matlab 8.2 to run segmentHA_T1_long.sh SUBJ1_basetemplate segmentHA_T1_long.sh SUBJ2_basetemplate etc I got an error in most of these jobs (mostly for templates of subjects with multiple visits) that read "ERROR: MatlabObjectArray(0x7fd7ce84cea0): Trying to access non-existing object (25) Error in kvlGetOptimizer (line 11) Error in SegmentSubfieldsT1Longitudinal (line 1155)” 2. I then tried running the cross sectional pipeline for each one of the timepoints in subjects already processed by the reconall longitudinal pipeline (i. e. segmentations in the .long. directories) segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_basetemplate segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_basetemplate segmentHA_T1.sh SUBJ2_timepoint1.long.SUBJ2_basetemplate segmentHA_T1.sh SUBJ3_timepoint1.long.SUBJ3_basetemplate etc Most of them ran without errors, but some still did. 3. I then tried to run the cross sectional hippocampal module for all subjects/timepoints without using the reconall longitudinal pipeline segmentHA_T1.sh SUBJ1_timepoint1 segmentHA_T1.sh SUBJ1_timepoint2 segmentHA_T1.sh SUBJ2_timepoint1 segmentHA_T1.sh SUBJ3_timepoint1 etc They were processed without errors. But when inspecting the processing log, there was a message that appeared 4 times in the file "WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! ……… …….. …... Everything done! It took 766.0135 seconds “ With manual inspection, subfield segmentations output by fs60 seemed fine in all the directories of the reconall cross sectional and longitudinal outputs (hippoSfLabels-T1). For the Hippocampal Module outputs (hippoAmygLabels-T1), the hippocampus was abbruptly cut, sometimes laterally, sometimes dorsally. This was the case for all three analyses. I wonder what is the problem and what I can do to fix it so I can successfully run the longitudinal pipeline of the "hippocampal subfields and nuclei of amygdala” Thanks for your help! Aura M.
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