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

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

External Email - Use Caution

That's super.

Thanks again Eugenio,

Best regards

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: 11 September 2018 16:44:34 To: Freesurfer support list; Freesurfer support list Subject: Re: [Freesurfer] Using the new Thalamus tool

External Email - Use Caution

10-15 mins or so

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: Tuesday, September 11, 2018 12:32:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Using the new Thalamus tool

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

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

External Email - Use Caution

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

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.

Erik O'Hanlon Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

On 09/11/2018 07:32 AM, Erik O'Hanlon wrote:

    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/

---

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