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Thanks Jim, The segmentations look nice, though the head is slightly undersegmented in the right hippo. You can barely discern the molecular layer so, even though the subfields surely carry useful information, they won’t be as precise as with a dedicated acquisition. 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 "Alexopoulos, Dimitrios" dimitriosalexopoulos@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 20 April 2018 at 17:46 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] using T2 for hippo subfields
External Email - Use Caution Eugenio,
I have uploaded a dataset for you to review. The file is ‘chd_auck_Bs44_6yr_fs.zip’. It was processed with the following command using FS 6.0. The native resolution is 0.82x0.82x0.85mm
recon-all -s chd_auck_BS44_6yr_fs -i T1..dcm -hippocampal-subfields-T1 -hires -all -qcache
Jim
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From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Friday, April 20, 2018 9:23 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] using T2 for hippo subfields
External Email - Use Caution Of course! https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
-- 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 20 April 2018 at 14:44 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] using T2 for hippo subfields
External Email - Use Caution Thanks for the input Eugenio.
Could you review one of our submillimeter T1 datasets processed using FS6.0? If yes, where can I upload to?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Friday, April 20, 2018 7:58 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] using T2 for hippo subfields
External Email - Use Caution You can but recon-all will resize to 1mm isotropic and you’ll lose your submil resolution. Of course, you could technically also use recon-all at 1mm, and then use the submil T1 as additional volume, but that’d be a bit inefficient…
-- 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 20 April 2018 at 13:47 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] using T2 for hippo subfields
External Email - Use Caution Ok. Can you run -hippocampal-subfields-T1 without the -hires flag using a submillimeter T1?
Jim ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Sent: Friday, April 20, 2018 2:24:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] using T2 for hippo subfields
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Sorry, I’m not sure I follow. But, if you run recon-all with the hires flag, then you can just run –hippo-subfields-T1 and it’ll take advantage of the high resolution.
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 20 April 2018 at 01:34 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] using T2 for hippo subfields
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Yes the output appears ok. I was under the impression there would be benefits from using the -hires flag with submillimeter T1s as input.
If you suggest not having to use the -hires flag in our case (because of little benefit from 0.8mm input compared to 1mm), I presume I can still use the -hippocampal-subfields-T1 option in the traditional recon-all -all stream?
Jim
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Sent: Thursday, April 19, 2018 1:57:18 PM To: Freesurfer support list Subject: Re: [Freesurfer] using T2 for hippo subfields
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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, Dimitriosmailto:freesurfer-bounces@nmr.mgh.harvard.edu%20on%20behalf%20of%20Alexopoulos,%20Dimitrios" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of dimitriosalexopoulos@wustl.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%20on%20behalf%20of%20dimitriosalexopoulos@wustl.edu> wrote:
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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.edumailto: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.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alexopoulos, > Dimitrios <dimitriosalexopoulos@wustl.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias > Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" > <dimitriosalexopoulos@wustl.edumailto:dimitriosalexopoulos@wustl.edu> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> > Date: Friday, 23 March 2018 at 16:00 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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 > > > > > > > > > > > > > ______________________________________________________________________ > ______________________________ > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > > > > ______________________________________________________________________ > ______________________________ > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > > > > ______________________________________________________________________ > ______________________________ > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If > you are not the intended recipient, be advised that any unauthorized > use, disclosure, copying or the taking of any action in reliance on > the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. > > >
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