Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

What would be the command for hippocampal subfields using only the T2 images?

 This? 

 recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>

I tried but obtained the following error 

pcpb3846:~ lab1-rmn$ recon-all -s /Applications/freesurfer/subjects/4235_T2 -hippocampal-subfields-T2 T2 T2_3D_SAG

ERROR: cannot find T2

Darwin pcpb3846.inv.usc.es 15.6.0 Darwin Kernel Version 15.6.0: Tue Jan 30 11:45:51 PST 2018; root:xnu-3248.73.8~1/RELEASE_X86_64 x86_64

recon-all -s 4235_T2 exited with ERRORS at Fri May  4 10:43:04 CEST 2018

Thanks

cheers,

2018-05-04 10:00 GMT+02:00 Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>:

        External Email - Use Caution        

Sorry if I didn’t explain myself properly.

T2 scans of the whole head can be used by recon-all to improve the segmentation of the pial surface, but:  a) They are not required (you can use the T1 alone); and b) Cannot be run through recon-all independently from the T1.

For hippocampal subfields: the T2 scan is used in a separate stream. In fact, their field of view doesn’t even have to cover the whole head – just the hippocampi (this is what the ADNI highres T2 protocol does).

Cheers,

/Eugenio

 

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of M Janani <jananimj@hcl.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 4 May 2018 at 08:26
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

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

 

        External Email - Use Caution        

Thanks for your reply Eugenio.

You have mentioned like “No recon-all on the T2 required, as it's used in a different way”. May I know the actual purpose of using T2 images for reconstruction process. Why we should not T2 images as input for recon-all command.

Regards,

Janani

 

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio
Sent: 04 May 2018 12:50
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: 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

 

        External Email - Use Caution        

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.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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