Hello,
I am trying to use the hippocampal subfield segmentation presented in the Iglesias paper. I downloaded and installed the latest available dev version about a week ago, along with FSL and the Matlab 2012b runtime. I attempted to run the pipeline and the hippocampal subfield segmentation together. The primary pipeline ran successfully as indicated by the log as well as manually checking the output in freeview. The hippocampal subfield segmentation did not complete successfully and the subsequent output files are nowhere to be found.
I checked the archive and saw that someone had a similar issue back in October. Based on the archive I have done the following trouble shooting steps:
1) I made sure that /Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib does exist.
2) I also tried unsetting the DYLD_LIBRARY_PATH as followed:
In bash:
unset DYLD_LIBRARY_PATH
In (t)csh:
unsetenv DYLD_LIBRARY_PATH
Then I reran the hippocampal segmentation as follows:
recon-all -s [subject] -hippocampal-subfields-T1
Still no success and not sure what else I can do. I am including both the recon-all.log and hippocoampal-subfields-T1.log.
Best,
Eric Nelson
Neuroimaging and Translational Research Lab
UAB