Matt,

Yes, I think the plan is to discuss this and other potential options. I had a feeling you may know the most, but I thought I would send out the question in case anyone else has tried. As it stands, it sounds like no method currently exists for a Caret surface-to-Freesurfer transition?

I am still trying to understand Freesurfer basics, but it sounds like the longitudinal pipeline generally requires the same input data as across-subject. My hope is that, since the surfaces are already constructed, I can avoid the need for an (infant) atlas, but I am still figuring out what that means in terms of files I need/conversion/etc.

Thanks for your help, and I look forward to further discussion this afternoon.

Kara

________________________________________ From: Matt Glasser [matt@ma-tea.com] Sent: Thursday, March 14, 2013 7:14 PM To: Bruce Fischl; Ellspermann, Kara Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Caret to Freesurfer

She wants to go from Caret to FreeSurfer, rather than from FreeSurfer to Caret, which is what I do.

Kara, I believe we are meeting tomorrow to discuss the options for this?

I don't know anything about the FreeSurfer longitudinal pipeline, but it would take going through the pipeline and finding all of the inputs needed and converting them or generating them. I think the main goal here is to use the longitudinal surface registration.

Matt.

On 3/14/13 8:04 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi Kara

I think the answer is yes as there are people at Wash U that do this routinely. Maybe Matt Glasser or someone else can chime in?

cheers Bruce

On Thu, 14 Mar 2013, Ellspermann, Kara wrote:

...

I am new to Freesurfer, and I am trying to input/process preterm infant brain data (ultimately attempting longitudinal registration). I already have surfaces generated from Caret, as well as the original T1/T2 images. My question is: Does anything exist to take processed data from Caret into Freesurfer? If not, is there a good way to process the T1/T2 images in Freesurfer despite the differences in contrast and intensity (and anatomy)?

Thank you in advance for your advice, Kara

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