Thanks Douglas,
I'll be sure to run my recon-all with the stable version and then run the rest on a second run.
Thanks for the help.
Cheers
Erik
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: 11 September 2018 18:12:39
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using the new Thalamus tool
Sent: 11 September 2018 18:12:39
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using the new Thalamus tool
And just to be clear, you should run only the thalamus, hippo, amyg,
brainstem segmentations in dev. Do not run recon-all using the dev version.
>
> External Email - Use Caution
>
> Thanks Eugenio,
>
>
> I'll intall the latest dev version so. How long does it typically take
> to run a subject through the thalamus pipeline typically?
>
>
> Thanks again for the prompt reply. Very much appreciated.
>
>
> Cheers
>
>
> Erik
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias
> Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>
> *Sent:* 10 September 2018 18:00:20
> *To:* freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
> *Subject:* Re: [Freesurfer] Using the new Thalamus tool
>
> External Email - Use Caution
>
> Dear Erik,
> Installing only the thalamic tool is technically possible but requires
> a level of hacking that i don't want to encourage or support ;-)
> Please install the new dev on a separate directory, and make
> FREESURFER_HOME point to that the directory (and source freesurfer) to
> run the thalamic tool. No need to rerun recon-all on the subjects.
> Cheers
> Eugenio
>
> Sent from my phone, please excuse brevity and typos
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon
> <erikohanlon@rcsi.ie>
> *Sent:* Thursday, September 6, 2018 3:44:57 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Using the new Thalamus tool
>
> External Email - Use Caution
>
> Hi FS Experts
>
>
> I've run my data through the brainstem, hippocampus and amygdala
> following the usual Recon_all and using the developmental version
> downloaded and stalled around Jan2018. I'd like to use the new
> thalamus tool and am wondering if I need to do a full install of the
> latest DEV version to do so. As I am still working on certain aspects
> of the analyses I've run so far, I don't want to overwrite my main FS
> installation mid analysis. Is it possible to download the toolbox and
> add it to my current dev version or is it best just to do another
> install with teh complete new Dev version? Is it possible to run the
> Thalamus analysis as an addtional component without having to rerun
> the recon_all again?
>
>
> Thanks and regards
>
>
> Erik
>
>
> *Erik O'Hanlon*
> Postdoctoral researcher
>
> *RCSI* Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont D9 Ireland
> *T: *8093740
> *E: *erikohanlon@rcsi.ie *W: *www.rcsi.com <http://www.rcsi.com/>
>
> /Transforming Healthcare Education, Research and Service: RCSI
> Strategic Plan 2018-2022 <http://www.rcsi.ie/strategy2018>/
>
>
>
>
>
> *Erik O'Hanlon*
> Postdoctoral researcher
>
> *RCSI* Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont D9 Ireland
> *T: *8093740
> *E: *erikohanlon@rcsi.ie *W: *www.rcsi.com <http://www.rcsi.com/>
>
> /Transforming Healthcare Education, Research and Service: RCSI
> Strategic Plan 2018-2022 <http://www.rcsi.ie/strategy2018>/
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
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brainstem segmentations in dev. Do not run recon-all using the dev version.
Erik O'Hanlon
Postdoctoral researcher
RCSI
Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohanlon@rcsi.ie W: www.rcsi.com
Transforming
Healthcare Education, Research and Service: RCSI Strategic Plan
2018-2022
>
> External Email - Use Caution
>
> Thanks Eugenio,
>
>
> I'll intall the latest dev version so. How long does it typically take
> to run a subject through the thalamus pipeline typically?
>
>
> Thanks again for the prompt reply. Very much appreciated.
>
>
> Cheers
>
>
> Erik
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias
> Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>
> *Sent:* 10 September 2018 18:00:20
> *To:* freesurfer@nmr.mgh.harvard.edu; Freesurfer support list
> *Subject:* Re: [Freesurfer] Using the new Thalamus tool
>
> External Email - Use Caution
>
> Dear Erik,
> Installing only the thalamic tool is technically possible but requires
> a level of hacking that i don't want to encourage or support ;-)
> Please install the new dev on a separate directory, and make
> FREESURFER_HOME point to that the directory (and source freesurfer) to
> run the thalamic tool. No need to rerun recon-all on the subjects.
> Cheers
> Eugenio
>
> Sent from my phone, please excuse brevity and typos
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon
> <erikohanlon@rcsi.ie>
> *Sent:* Thursday, September 6, 2018 3:44:57 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Using the new Thalamus tool
>
> External Email - Use Caution
>
> Hi FS Experts
>
>
> I've run my data through the brainstem, hippocampus and amygdala
> following the usual Recon_all and using the developmental version
> downloaded and stalled around Jan2018. I'd like to use the new
> thalamus tool and am wondering if I need to do a full install of the
> latest DEV version to do so. As I am still working on certain aspects
> of the analyses I've run so far, I don't want to overwrite my main FS
> installation mid analysis. Is it possible to download the toolbox and
> add it to my current dev version or is it best just to do another
> install with teh complete new Dev version? Is it possible to run the
> Thalamus analysis as an addtional component without having to rerun
> the recon_all again?
>
>
> Thanks and regards
>
>
> Erik
>
>
> *Erik O'Hanlon*
> Postdoctoral researcher
>
> *RCSI* Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont D9 Ireland
> *T: *8093740
> *E: *erikohanlon@rcsi.ie *W: *www.rcsi.com <http://www.rcsi.com/>
>
> /Transforming Healthcare Education, Research and Service: RCSI
> Strategic Plan 2018-2022 <http://www.rcsi.ie/strategy2018>/
>
>
>
>
>
> *Erik O'Hanlon*
> Postdoctoral researcher
>
> *RCSI* Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont D9 Ireland
> *T: *8093740
> *E: *erikohanlon@rcsi.ie *W: *www.rcsi.com <http://www.rcsi.com/>
>
> /Transforming Healthcare Education, Research and Service: RCSI
> Strategic Plan 2018-2022 <http://www.rcsi.ie/strategy2018>/
>
>
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cerikohanlon%40rcsi.ie%7C5054bee0dc7c40e204ae08d61809f843%7C607041e7a8124670bd3030f9db210f06%7C0%7C0%7C636722828434630922&sdata=XVY5uESPLfsTzpCcZTMRLFWr4S2LfaTKl8SJi16RT9U%3D&reserved=0
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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
https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.partners.org%2Fcomplianceline&data=02%7C01%7Cerikohanlon%40rcsi.ie%7C5054bee0dc7c40e204ae08d61809f843%7C607041e7a8124670bd3030f9db210f06%7C0%7C0%7C636722828434630922&sdata=827SWhIhvG31KifL0j4NQTa6PSj6qFGEdZ%2FXe30LdY0%3D&reserved=0 . 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.