On 2016. 1. 21., at 오전 6:35, Eugenio Iglesias <e.iglesias@bcbl.eu> wrote:

Sorry, it wasn't clear from the previous email whether the left hemi had completed or not.

Can you please send me the recon-all log file?

Cheers,

/E

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

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

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From: "Jiook Cha" <cha.jiook@gmail.com>
To: "Eugenio Iglesias" <e.iglesias@bcbl.eu>
Cc: "iglesias" <iglesias@nmr.mgh.harvard.edu>, "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, January 21, 2016 12:32:46 PM
Subject: Re: HippocampalSubfields only generates lh

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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