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Hey Freesurfer folks,
I'm running into a strange error with the TRACULA longitudinal stream, whereby all of the steps run "without error" but the final merged paths look like a collection of single voxels (see screenshot below). The individual paths typically show up as single or a few voxels as well. This seems to be happening on all/most of my subjects. I've checked the outputs from trac-all -prep and the FA volumes look right. I've also QAed all of the cortical surface recons and they look good. Also, the individual tract streamlines (the .trk files) look pretty reasonable (see second screenshot). So, I'm assuming that this is an issue at -path step when converting the .trk files to volumes, but am unsure how to troubleshoot it. I'm assuming that the path stats that are output are derived from the volumes and not the streamlines, so this is probably an important step to correct, right?
Just FYI, I'm running freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b on Ubuntu 18.04.4 LTS and FSL v4 (FSL v5.0 won't work with the trac-all -prep commands for me) and I run bedpost directly on the dmri folder (I have an SGE cluster). Any chance you've seen this error before?
Thanks in advance for any advice! David
merged path volumes:
several of the streamline files from the same subject:
