Hi Eugenio,

I think he is just after cortical surfaces.

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Iglesias, Eugenio" e.iglesias@ucl.ac.uk Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, June 10, 2016 at 12:30 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] using both T1/T2 and resolutions

Hi! I actually sent out an email yesterday regarding this. The way that the subfield module is set up, you cannot take advantage of your full res T1 and your T1. We are working on a solution. Cheers, Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 10 Jun 2016, at 17:04, Matt Glasser matt@ma-tea.com wrote:

Hi Jim,

I would just use the HCP Pipelines for that: https://github.com/Washington-University/Pipelines, as they take care of all of those things re FreeSurfer. I would set to using the 0.8mm templates so that nothing is down sampled.

Peace,

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Alexopoulos, Dimitrios" Alexopoulos_D@kids.wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, June 10, 2016 at 10:56 AM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] using both T1/T2 and resolutions

Hi,

We¹d like to process pediatric data through the complete FS 5.3 pipeline. The T1/T2 data are acquired with a 3T Siemens as follows: T1 mpr sag - 0.82x0.82x0.85 T2 Space - 1x1x1

We¹d like to process using both the T1 and T2 (for better dura removal and possible myelin analysis). Is it possible to use the hires T1 and have data not downsampled to 1x1x1? Ifpossible, can this be done in tandem with the lower resolution T2-space?

What recon-all command would be best for this process?

Jim

The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. _______________________________________________ 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 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 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.

I'm interested in getting both the most accurate cortical surfaces and volumetrics.

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Friday, June 10, 2016 12:54 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] using both T1/T2 and resolutions

Hi Eugenio,

I think he is just after cortical surfaces.

Matt.

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias, Eugenio" <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, June 10, 2016 at 12:30 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] using both T1/T2 and resolutions

Hi! I actually sent out an email yesterday regarding this. The way that the subfield module is set up, you cannot take advantage of your full res T1 and your T1. We are working on a solution. Cheers, Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 10 Jun 2016, at 17:04, Matt Glasser <matt@ma-tea.commailto:matt@ma-tea.com> wrote:

Hi Jim,

I would just use the HCP Pipelines for that: https://github.com/Washington-University/Pipelines, as they take care of all of those things re FreeSurfer. I would set to using the 0.8mm templates so that nothing is down sampled.

Peace,

Matt.

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <Alexopoulos_D@kids.wustl.edumailto:Alexopoulos_D@kids.wustl.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, June 10, 2016 at 10:56 AM To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] using both T1/T2 and resolutions

Hi,

We'd like to process pediatric data through the complete FS 5.3 pipeline. The T1/T2 data are acquired with a 3T Siemens as follows: T1 mpr sag - 0.82x0.82x0.85 T2 Space - 1x1x1

We'd like to process using both the T1 and T2 (for better dura removal and possible myelin analysis). Is it possible to use the hires T1 and have data not downsampled to 1x1x1? Ifpossible, can this be done in tandem with the lower resolution T2-space?

What recon-all command would be best for this process?

Jim

The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 Freesurfer@nmr.mgh.harvard.edumailto: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 Freesurfer@nmr.mgh.harvard.edumailto: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.