From Ganjizadeh.Ali@mayo.edu Wed Dec 27 22:04:14 2023
From: "Ganjizadeh, Ali, M.D." <Ganjizadeh.Ali@mayo.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Brainstem segmentation without pre-processing
Date: Thu, 28 Dec 2023 03:04:00 +0000
Message-ID: <d2a753$l703ji@ironport10.mayo.edu>
MIME-Version: 1.0
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        External Email - Use Caution       =20

Good evening,
I am trying to work with segmentBS.sh. I want to pass my .nii.gz files that a=
re already pre-processed with HD-BET, but I don't want to use recon-all as th=
e first step because it takes a lot of time. I also tried recon-all -autoreco=
n2 and 3, but it resulted in an error.

Is there any specific command that I will be able to pass my files directly t=
o segmentBS.sh? Or is there any command for recon-all to only make subjects w=
ithout processing or fast processing?

Thank you,
Ali


Ali Ganjizadeh, M.D. (he/him)

Postdoctoral Research Fellow

Mayo AI Lab (Radiology Information Lab)

Mayo Clinic-Rochester



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From JIGLESIASGONZALEZ@mgh.harvard.edu Thu Dec 28 10:20:16 2023
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Brainstem segmentation without pre-processing
Date: Thu, 28 Dec 2023 15:20:16 +0000
Message-ID: <PH0PR04MB8388A832DA8812959D2EC718FD9EA@PH0PR04MB8388.namprd04.prod.outlook.com>
In-Reply-To: <d2a753$l703ji@ironport10.mayo.edu>
MIME-Version: 1.0
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--===============0762043152715938807==
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: quoted-printable

Dear Ali,
Making a SynthSeg version of the tool is on the to-do list but has not happen=
ed yet. For now, you need to run recon-all. The good news is that you get a t=
on of additional useful information on the brains!
Kind regards,
/Eugenio

--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.=
harvard.edu> on behalf of Ganjizadeh, Ali, M.D. <Ganjizadeh.Ali(a)mayo.edu>
Date: Wednesday, December 27, 2023 at 22:04
To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>
Subject: [Freesurfer] Brainstem segmentation without pre-processing

        External Email - Use Caution
Good evening,
I am trying to work with segmentBS.sh. I want to pass my .nii.gz files that a=
re already pre-processed with HD-BET, but I don't want to use recon-all as th=
e first step because it takes a lot of time. I also tried recon-all -autoreco=
n2 and 3, but it resulted in an error.

Is there any specific command that I will be able to pass my files directly t=
o segmentBS.sh? Or is there any command for recon-all to only make subjects w=
ithout processing or fast processing?

Thank you,
Ali


Ali Ganjizadeh, M.D. (he/him)

Postdoctoral Research Fellow

Mayo AI Lab (Radiology Information Lab)

Mayo Clinic-Rochester



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--===============0762043152715938807==--


