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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