Hi Flavia, Did the hippo subfield routine complete successfully? Are the outputs in the mri directories of the subjects? Did you look at the log files of the subfield routine? Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Loreto, Flavia" f.loreto@imperial.ac.uk Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, March 18, 2020 at 08:28 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri hippocampal subfields:output file
External Email - Use Caution 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