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
------------------------------------------------------------------------
*From:* Juan Eugenio Iglesias <igles...@nmr.mgh.harvard.edu>
*To:* Irene Lee <lee.iren...@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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http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.
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