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

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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