Hi Erik,
30 mins for a subject sounds correct. If the text files with the volumes are
there, and the segmentations look plausible, then everything should be fine.
One more thing: it the outputs are in specific directories, please note that we
changed the naming convention and structure of the output last week - sorry
about that! We believe that the changes made the module easier to use. Please
see the updated instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
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: Wednesday, May 27, 2015 10:17:51 AM
Subject: Re: [Freesurfer] hippocampal subfields
Hi Eugenio,
I managed to get the subfield code process to run, my cluster wasn't using all
the allotted RAM for the job, thank you for all the input. Can I ask how long
it typically takes as it appears to have completed in about 30mins and gave me
the left and right dirs with the volume txts etc. Just wanted to be sure before
I kick it off on the complete data set.
Thanks again for all the help.
Cheers
Ertik
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: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]
Sent: 26 May 2015 11:25
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
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>
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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 "
target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was
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><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>
<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>
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>
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>
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The information in this e-mail is intended only for the person to whom it is
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The information in this e-mail is intended only for the person to whom it is
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