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Dear FreeSurfer experts,

Version: FreeSurfer 6.0 Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave

We have run hippocampal subfields segmentation analyses and we are now having problems exporting the volumetric outputs. We have run Iglesias’ ‘obsolete’ script to obtain hippocampal volumes, as our system does not support the dev version of Freesurfer.

recon-all -all -s bert -hippocampal-subfields-T1

Then, to gather volumes from our analysed subjects, we have run this script

quantifyHippocampalSubfields.sh <T1>-<analysisID> <output_file> <OPTIONAL_subject_directory>

In particular, this is how it looks in our terminal: -bash-4.2$ quantifyHippocampalSubfields.sh T1 hippo_demo.txt /rds/general/project/amyloidpet/live/freesurfer Gathering results from subjects in: /rds/general/project/amyloidpet/live/freesurfer Using the suffix name: T1 And writing them to: hippo_demo.txt

However, we are not able to find the output anywhere. Could you help us figuring out what could be the reason why can’t find it? I have attached the recon-all.log for one of our analysed subjects.

Many thanks for your help. Kind regards, Flavia