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Thanks. I ran several subjects that were native 0.82 x 0.82 x 0.85mm through the standard recon-all -all stream, with the -hires flag (but with no experts file). The volumes and surafces look good. Is there any need to be concerened with the output since I did not use an experts file?
Jim
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, April 04, 2018 7:52 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] using T2 for hippo subfields
no it is not required
cheers Bruce On Wed, 4 Apr 2018, Alexopoulos, Dimitrios wrote:
Per an earlier post below, is an 'expert_file' always required when using the -hires option?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios dimitriosalexopoulos@wustl.edu Sent: Sunday, March 25, 2018 9:47:07 PM To: Freesurfer support list Subject: Re: [Freesurfer] using T2 for hippo subfields
Thanks for the input. I processed a few subjects (T1-mprage, 0.8mm isotropic) using the -hires flag, with no expert file, which generated nice surfaces.
Is an 'expert_file' required ??
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk Sent: Friday, March 23, 2018 11:02:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] using T2 for hippo subfields
Hi Jim,
In the end it's an empirical question, but my gut feeling is that the T1 with hi-res flag will be best.
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Alexopoulos, Dimitrios" dimitriosalexopoulos@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 23 March 2018 at 16:00 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] using T2 for hippo subfields
Hi. We are acquiring sequences on a pediatric cohort that include a T1-mprage (0.8mm isotropic) and a T2-space (1mm isotropic), and I'd like to run the hippocampal subfields module on the subjects using FS 6.0.
Is it recommended/useful to run the multispectral segmentation mode with the additional lower resolution T2 sequence?
I read that you really only benefit if the T2 is of similar or better resolution than the T1.
If that's the case, would it be best to just run with the single T1 but with the hi-res flag in the recon-all command?
Thanks.
Jim
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