Thanks Bruce,
Much appreciated
Best regards
Erik
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: 03 February 2017 15:18
To: Freesurfer support list
Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags
(freesurfer v6) {Disarmed}
Hi Erik
Eugenio can confirm, but I don't think the subfield stuff cares. The
-hippocampal-subfields-T1T2 means use multiple inputs, but it doesn't
assume anything about the distribution of intensities in them.
cheers
Bruce
On Fri, 3 Feb
2017, Erik O'Hanlon wrote:
> Hi Experts,
>
> Just flowing on from Joe's question, I have run my analysis without the T2 or
> FLAIR flag but have
> specificed the T2 which is a FLAIR image for the hippocampal subfield
> options. I have used
>
> recon-all -all -3T -s /sub008 -hippocampal-subfields-T1T2
> /sub008/sub_008_T2.nii.gz T2Flair
>
> Should I have used -hippocampal-subfields-T1FLAIR instead? Can I change this
> and simply rerun without
> the need to do everything from scratch.
> I have T2 and FLAIR images that I havent used for pial correction, can I add
> that in too and if so which
> is best teh T2 or the FLAIR or both?
>
> Thanks and as always, really appreciate the help
>
> Cheers
>
> Erik
>
> ________________________________________________________________________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Joe
> Necus (PGR) [j.nec...@newcastle.ac.uk]
> Sent: 03 February 2017 10:56
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags
> (freesurfer v6) {Disarmed}
>
> Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag.
>
>
> Joe
>
>
>
> Erik O'Hanlon
> Postdoctoral researcher
>
> [IMAGE]
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
>
>
>
> ________________________________________________________________________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce
> Fischl <fis...@nmr.mgh.harvard.edu>
> Sent: 02 February 2017 22:56
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags
> (freesurfer v6)
> Hi Joe
>
> there are slight differences, and for sure we reserve the right to use
> the knowledge that it is a FLAIR scan in the algorithms, so you should
> probably rerun
>
> cheers
> Bruce
> On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:
>
> >
> > Hello,
> >
> >
> > I am running recon-all on the latest version of freesurfer (Version 6) and
> > would like to know whether
> > there is any difference between using the -T2 -T2Pial and -Flair flags.
> >
> >
> > I am currently running recon-all with a T1 and FLAIR image, but have used
> > the -T2 -T2pial flags and
> > would like to know whether I need to go back and instead re-run with the
> > -FLAIR flag instead.
> >
> >
> > Thanks a lot,
> >
> > Joe
> >
> >
> >
> >
> >
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