Hi again, Irene,

On 10/03/2013 09:39 AM, Irene Lee wrote:

Hi, Eugenio,

I have already sent the log files to you.

Sorry, I should have been more specific. I meant [subject_dir]/scripts/recon-all.log and [subject_dir]/scripts/hippo-subfields.log

And would you please give me a hint what is the right command for computing subfields with high-res T2? Thank you very much!!

This is not an option at this point, but we are working on it.

Cheers,

/Eugenio

-Irene

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*From:* Juan Eugenio Iglesias iglesias@nmr.mgh.harvard.edu *To:* Irene Lee lee.irene49@yahoo.com *Cc:* "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Sent:* Tuesday, October 1, 2013 4:37 PM *Subject:* Re: [Freesurfer] Hippocampal subfield segmentation paused

Hi Irene, two things:

1. Can you please send us the log files of the recon?
2. The command you executed will compute the subfield segmentation

based only on the T1, not the high-res T2. Cheers, /Eugenio

On 10/01/2013 04:30 PM, Irene Lee wrote:

...

Hi, there,

I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas.

Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation

I used the command

recon-all -s my subject -all -hippo-subfields

It was running well, however, it halted/paused after it displayed the following information:"final transformation (x=..,yr=..,zr=..) and a 4x4 matrix".

For a week it is not going anywhere and not producing any output.

The computer I was running it on had sufficient computational resources and a Fedora linux system. It does not seem to be related to the configuration of the computer.

Has anyone ever encountered this problem?? Any diagnostic advice will be appreciated!!

-Irene

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