Thank you, Victor. 1.5x1x1mm is not ideal, but you should be able to run the modules. Just make sure to QC the output.

Cheers,

/Eugenio

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" <vzeng@bidmc.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, July 2, 2020 at 16:02
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: "joliehoang22@gmail.com" <joliehoang22@gmail.com>
Subject: Re: [Freesurfer] Subfield parcellation in 1.5 T and 2.6 mm Thickness {Disarmed}

The original MRI dims were: 256 256 124, 

and pixel dim: 0.9375 0.9375 1.5

These MRI scans are really old and predate DCMs so I'm not exactly sure how else to extract the data. But there's no complementary MR scans included in the FS processing either. 

I have mixed sources saying different things for the thickness (I'm assuming the thickness is 1.5). I am told that the fov is 240, but I'm not sure how I can confirm. 

Victor Zeng

Beth Israel Deaconess Medical Center

Keshavan Lab

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu>
Sent: Thursday, July 2, 2020 2:55 PM
To: Freesurfer support list
Cc: joliehoang22@gmail.com
Subject: [External] Re: [Freesurfer] Subfield parcellation in 1.5 T and 2.6 mm Thickness

Dear Victor,

Sorry for the slow response.

1.5 T is not a problem.

Do you have a companion 1mm T1?

If no: then the main problem is the main recon stream.

If yes: what is the in-plane resolution and orientation? If it’s a high-res coronal, it may help with the subfields. For the thalamus, I’d just use the 1 mm T1.

Cheers,

/Eugenio

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be http://www.jeiglesias.com

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" <vzeng@bidmc.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, June 25, 2020 at 17:56
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: "joliehoang22@gmail.com" <joliehoang22@gmail.com>
Subject: [Freesurfer] Subfield parcellation in 1.5 T and 2.6 mm Thickness

Hi FS developers,

We were wondering whether a MRI scan that has 2.6 mm thickness + is 1.5 T would be sufficient for a subfield analysis (amygdala, hippocampus, thalamus).

Thanks,

Victor Zeng

Beth Israel Deaconess Medical Center

Keshavan Lab

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