Hi, Eugenio,

I have already sent the log files to you. And would you please give me a hint what is the right command for computing subfields with high-res T2? Thank you very much!!

-Irene


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:

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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Juan Eugenio Iglesias, PhD
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iglesias@nmr.mgh.harvard.edu
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