Re: [Freesurfer] T2 weighted images as input for recon-all command

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Hola Miguel Ángel, First, you need to run the T1 through recon-all normally, as you have already done. Next, you run the subfield module with the highres T2 as input - no recon-all on the T2 required, as it's used in a different way. 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 Miguel Ángel Rivas Fernández miguelrivasfdez@gmail.com Sent: Thursday, May 3, 2018 11:08:17 PM To: Freesurfer support list Subject: Re: [Freesurfer] T2 weighted images as input for recon-all command

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Hi Freesurfer developers,

I have executed the recon-all command using the T1 images but I would be interested in doing a reconstruction of the hippocampal subregions using for that purpose a higher resolution images (eg T2 or FLAIR) as input. I read here https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields that is possible make hippocampal segmentation using the T2 images, but if T2 images cannot be used as input to execute the recon-all in consecuence I can´t do the segmentation of hippocampal subfields or on the contrary the recon-all and the hippocampal subfields segmentation are two operations that can be executed independently ?

I hope to have explained myself correctly

Thanks in advance.

Cheers

2018-05-03 18:28 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu>: No, not currently

On 05/03/2018 11:26 AM, M Janani wrote:

Hi Team,

           I have one doubt. Can I input T2 weighted images for

recon-all command?

Regards,

Janani

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