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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joe Necus (PGR) [J.Necus2@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

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohanlon@rcsi.ie W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@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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