Hi again,
The software requires approximately 10GB of RAM
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: Tue, 26 May 2015 12:16:00 +0200 (CEST)
Subject: Re: [Freesurfer] hippocampal subfields
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<div class="PlainText">Hi Eugenio,<br>
<br>
I'm trying to run in on a cluster and I think I have eight cores assigned
with 2GB per core. I'm not sure if the process is parallelised though so it
could be the case that I have the job running on one of the possible core and
only using 2GB of RAM. I can
ask the cluster support team to check but is it possible to run the job across
the 8 cores and thus grab the 16GB of RAM or will the code only use the
one core and I will have to get the RAM assigned to it to be
increased.<br>
<br>
Any guidance much appreciated and maybe if you could outline a typical system
requirement/setup to run a job. I have 200 subjects so your advice would
super.<br>
<br>
Thanks again<br>
<br>
Cheers<br>
<br>
Erik<br>
________________________________________<br>
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]<br>
Sent: 26 May 2015 10:33<br>
To: Freesurfer support list<br>
Subject: Re: [Freesurfer] hippocampal subfields<br>
<br>
Hi Erik,<br>
I guess your process was killed by the kernel. Maybe you ran out of RAM memory?
How much RAM do you have?<br>
Cheers,<br>
/Eugenio<br>
<br>
Juan Eugenio Iglesias<br>
Postdoctoral researcher BCBL<br>
<a href="http://www.jeiglesias.com"; target="_blank">www.jeiglesias.com</a><br>
<a href="http://www.bcbl.eu"; target="_blank">www.bcbl.eu</a><br>
<br>
Legal disclaimer/Aviso legal/Lege-oharra: <a
href="http://www.bcbl.eu/legal-disclaimer"; target="_blank">
www.bcbl.eu/legal-disclaimer</a><br>
<br>
<br>
----- Original Message -----<br>
From: "Erik O'Hanlon" <erikohan...@rcsi.ie><br>
To: "Freesurfer support list"
<freesurfer@nmr.mgh.harvard.edu><br>
Sent: Monday, May 25, 2015 6:53:54 PM<br>
Subject: Re: [Freesurfer] hippocampal subfields<br>
<br>
<br>
<br>
Hi FS Experts,<br>
<br>
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<br>
<br>
Making Unknown map to reduced label 13<br>
Computing hyperparameters for estimation of Gaussian parameters<br>
Estimating typical intensities of alveus<br>
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 43: 2675 Killed
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args<br>
~<br>
<br>
It appears that the process finished prematurely and didn't write out
anything in the mri/ dir.<br>
<br>
Any pointers how to resolve ? Any help greatly appreciated<br>
<br>
Cheers<br>
<br>
Erik<br>
<br>
Erik O'Hanlon<br>
Postdoctoral researcher<br>
<br>
<br>
<br>
<br>
RCSI Psychiatry<br>
Royal College of Surgeons in Ireland<br>
Beaumont Road, Beaumont, D9, Ireland<br>
T: 8093740<br>
E: erikohan...@rcsi.ie W: <a href="http://www.rcsi.ie";
target="_blank">www.rcsi.ie</a><br>
<br>
RCSI DEVELOPING HEALTHCARE LEADERS<br>
WHO MAKE A DIFFERENCE WORLDWIDE<br>
________________________________________<br>
From: Erik O'Hanlon<br>
Sent: 08 May 2015 19:10<br>
To: Freesurfer support list<br>
Subject: RE: [Freesurfer] hippocampal subfields<br>
<br>
That is super Nick,<br>
<br>
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?<br>
<br>
Thanks again for all the help<br>
<br>
Erik<br>
________________________________________<br>
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH
[ni...@nmr.mgh.harvard.edu]<br>
Sent: 08 May 2015 19:05<br>
To: Freesurfer support list<br>
Subject: Re: [Freesurfer] hippocampal subfields<br>
<br>
Erik,<br>
<br>
If you wanted to test a 'beta' of v6, which has the new hippocampal<br>
stream, then our current internal 'dev' build, which is very close
to<br>
being the upcoming v6, can be downloaded from here:<br>
<br>
<a href="ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/";
target="_blank">ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/</a><br>
<br>
This goes for anyone else on the list who would like to help us test v6<br>
prior to release.<br>
<br>
Nick<br>
<br>
<br>
On Fri, 2015-05-08 at 13:36 +0000, Erik O'Hanlon wrote:<br>
> Hi Eugenio,<br>
><br>
> That's brilliant, thanks so much for the quick response. So I will<br>
> download the v6 code and how do I call the command so that it runs the<br>
> v6 subfield analysis from the recon_all command?<br>
><br>
> Thanks again for the guidance. Very much appreciated<br>
><br>
> Cheers<br>
><br>
> Erik<br>
> ________________________________________<br>
> From: freesurfer-boun...@nmr.mgh.harvard.edu<br>
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias<br>
> [e.igles...@bcbl.eu]<br>
> Sent: 08 May 2015 13:16<br>
> To: Freesurfer support list<br>
> Subject: Re: [Freesurfer] hippocampal subfields<br>
><br>
> Hi Erik,<br>
> the 6.0 subfield code won't overwrite your 5.3 results, so if you
run<br>
> the 6.0 module on data analyzed with 5.3, both results will co-exist<br>
> in the MRI directory of each subject.<br>
> Kind regards,<br>
> /Eugenio<br>
><br>
> Juan Eugenio Iglesias<br>
> Postdoctoral researcher BCBL<br>
> <a href="http://www.jeiglesias.com";
target="_blank">www.jeiglesias.com</a><br>
> <a href="http://www.bcbl.eu"; target="_blank">www.bcbl.eu</a><br>
><br>
> Legal disclaimer/Aviso legal/Lege-oharra: <a
href="http://www.bcbl.eu/legal-disclaimer"; target="_blank">
www.bcbl.eu/legal-disclaimer</a><br>
><br>
><br>
> ----- Original Message -----<br>
> From: "Erik O'Hanlon" <erikohan...@rcsi.ie><br>
> To: freesurfer@nmr.mgh.harvard.edu<br>
> Sent: Friday, May 8, 2015 2:07:18 PM<br>
> Subject: [Freesurfer] hippocampal subfields<br>
><br>
><br>
><br>
> Hi FS experts,<br>
><br>
><br>
> I completed an analysis including the hippocampal subfield options<br>
> using 5.3.0. I understand that the subfield options was then removed<br>
> and I noticed that the new rev of the subfield code will be ready for<br>
> the v6 FS update. Can I use this code with my 5.3.0 code and if so<br>
> what files /dirs will I have to remove and how can I run or rerun it<br>
> to get the new subfield measures if it's possible. I would really
like<br>
> to obtain the subfield measures and am not sure if I can use the<br>
> existing measures based on the 5.3.0 code. Any advice would be very<br>
> much appreciated.<br>
><br>
><br>
> Kind regards and thanks in advance<br>
><br>
><br>
> Erik<br>
><br>
> Erik O'Hanlon<br>
> Postdoctoral researcher<br>
><br>
><br>
><br>
><br>
> RCSI Psychiatry<br>
> Royal College of Surgeons in Ireland<br>
> Beaumont Road, Beaumont, D9, Ireland<br>
> T: 8093740<br>
> E: erikohan...@rcsi.ie W: <a href="http://www.rcsi.ie";
target="_blank">www.rcsi.ie</a><br>
><br>
> RCSI DEVELOPING HEALTHCARE LEADERS<br>
> WHO MAKE A DIFFERENCE WORLDWIDE<br>
> _______________________________________________<br>
> Freesurfer mailing list<br>
> Freesurfer@nmr.mgh.harvard.edu<br>
> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer";
target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a><br>
><br>
><br>
> The information in this e-mail is intended only for the person to whom<br>
> it is<br>
> addressed. If you believe this e-mail was sent to you in error and the<br>
> e-mail<br>
> contains patient information, please contact the Partners Compliance<br>
> HelpLine at<br>
> <a href="http://www.partners.org/complianceline";
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><br>
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> Freesurfer mailing list<br>
> Freesurfer@nmr.mgh.harvard.edu<br>
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target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a><br>
<br>
<br>
_______________________________________________<br>
Freesurfer mailing list<br>
Freesurfer@nmr.mgh.harvard.edu<br>
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target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer</a><br>
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Freesurfer mailing list<br>
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<br>
<br>
The information in this e-mail is intended only for the person to whom it is<br>
addressed. If you believe this e-mail was sent to you in error and the
e-mail<br>
contains patient information, please contact the Partners Compliance HelpLine
at<br>
<a href="http://www.partners.org/complianceline";
target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was
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