Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory?
How much RAM do you have?
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
----- Original Message -----
From: "Erik O'Hanlon" <erikohan...@rcsi.ie>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, May 25, 2015 6:53:54 PM
Subject: Re: [Freesurfer] hippocampal subfields
Hi FS Experts,
I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0
and I encountered the following error in the log file
Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 43: 2675 Killed "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args
~
It appears that the process finished prematurely and didn't write out anything
in the mri/ dir.
Any pointers how to resolve ? Any help greatly appreciated
Cheers
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
________________________________________
From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields
That is super Nick,
I'll download it next week and try it out. Will I need to just run the subfield
part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?
Thanks again for all the help
Erik
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH
[ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Erik,
If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
This goes for anyone else on the list who would like to help us test v6
prior to release.
Nick
On Fri, 2015-05-08 at 13:36 +0000, Erik O'Hanlon wrote:
> Hi Eugenio,
>
> That's brilliant, thanks so much for the quick response. So I will
> download the v6 code and how do I call the command so that it runs the
> v6 subfield analysis from the recon_all command?
>
> Thanks again for the guidance. Very much appreciated
>
> Cheers
>
> Erik
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
> [e.igles...@bcbl.eu]
> Sent: 08 May 2015 13:16
> To: Freesurfer support list
> Subject: Re: [Freesurfer] hippocampal subfields
>
> Hi Erik,
> the 6.0 subfield code won't overwrite your 5.3 results, so if you run
> the 6.0 module on data analyzed with 5.3, both results will co-exist
> in the MRI directory of each subject.
> Kind regards,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> ----- Original Message -----
> From: "Erik O'Hanlon" <erikohan...@rcsi.ie>
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, May 8, 2015 2:07:18 PM
> Subject: [Freesurfer] hippocampal subfields
>
>
>
> Hi FS experts,
>
>
> I completed an analysis including the hippocampal subfield options
> using 5.3.0. I understand that the subfield options was then removed
> and I noticed that the new rev of the subfield code will be ready for
> the v6 FS update. Can I use this code with my 5.3.0 code and if so
> what files /dirs will I have to remove and how can I run or rerun it
> to get the new subfield measures if it's possible. I would really like
> to obtain the subfield measures and am not sure if I can use the
> existing measures based on the 5.3.0 code. Any advice would be very
> much appreciated.
>
>
> Kind regards and thanks in advance
>
>
> Erik
>
> Erik O'Hanlon
> Postdoctoral researcher
>
>
>
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
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> Freesurfer mailing list
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>
>
> The information in this e-mail is intended only for the person to whom
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_______________________________________________
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
