Yes they were. 



On Jan 21, 2016, at 06:14, Eugenio Iglesias <e.iglesias@bcbl.eu> wrote:

Hi Jiook,
the log file says that the analysis of the left side did complete. Were the output files written?
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

From: "Jiook Cha" <cha.jiook@gmail.com>
To: "iglesias" <iglesias@nmr.mgh.harvard.edu>
Cc: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, January 20, 2016 2:16:36 AM
Subject: HippocampalSubfields only generates lh

Hi Iglesias,

I recently tried HippocampalSubfields in freesurfer 6.0. It only completed hippocampal segmentation for the left hemisphere, but not the right. 

Under scripts folder, recon-all.error says:
/ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/recon-all
PWD /ifs/scratch/pimri/posnerlab/1anal/osa/fs2/B03/label
CMD /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/segmentSF_T1.sh /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/MCRv80 /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer B03 /ifs/scratch/pimri/posnerlab/1anal/osa/fs2 left

So it seems as left hippocampus failed the pipeline didn’t try the right hippocampus.

Attached is hippocampal-subfields-T1.log. Do you have any idea what’s happening here?












Best,

Jiook


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