Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

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

        External Email - Use Caution       

Hi Jim,
>From my experience .8 isotropic is on the edge. Did you take a look at the output? You can always send us the data if you want us to take a look.
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/
 

On 19/04/2018, 19:55, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dimitriosalexopoulos@wustl.edu> wrote:

            External Email - Use Caution       
   
    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
    >
    > http://www.jeiglesias.com
    >
    > http://cmictig.cs.ucl.ac.uk/
    >
    >
    >
    >
    >
    > 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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