External Email - Use Caution        

Thanks for getting back to me Doug/Bruce.
Sounds good, yes I definitely would want to wait until the bugs have been worked out before utilizing latest release.

If your dev team needs contributors to document/write the ex-vivo processing stream I'd be happy to step in and help, I've been running various ex-vivo scan acquisitions through freesurfer for a year at this point. I also have experience in C and shell scripting if that helps, as it seems that's what much of freesurfer is written in.
Not sure who I would talk to about that. 

Best,
Kody Zalewski

Message: 11
Date: Tue, 19 Mar 2019 14:53:30 +0000
From: "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
Subject: Re: [Freesurfer] Omitting aseg regions from segmentationTo: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <235d9f13-1eda-1d76-920f-d30b9c467635@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

... but know that the dev version is not fully tested -- there may be significant bugs that will not be uncovered until it is tested. As such, we may not be able to support any problems you run into.

On 3/18/19 8:12 PM, Bruce Fischl wrote:
Hi Kody

there definitely are flags like this in the dev version. e.g.:
    case "-no-cerebellum":
    case "-nocerebellum":
    case "-NO-CEREBELLUM":
    case "-NOCEREBELLUM":
    set nocerebellum=( -nocerebellum)
    breaksw ;

Maybe you should just grab the dev version?

And sorry, we haven't documented the ex vivo processing stream yet as it is too much of a work-in-progress.

cheers
Bruce
On Thu, 14 Mar 2019, zalewk wrote:


        External Email - Use Caution

Hi Bruce,

In response to your previous email, in v6.0 it doesn't look like recon-all has a "-no-cerebellum"
flag (or any cerebellum-related flags), I did verify that the recon-all script in the bin folder had
hemisphere-specific flags available however.

Is there any documentation on this? It still seems as if I'm missing something here, was it maybe
included in previous versions of freesurfer and removed?

Best,
Kody Zalewski

Date: Mon, 4 Mar 2019 15:07:26 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Omitting aseg regions from segmentation
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1903041505530.3767@gate.nmr.mgh.harvard.edu><mailto:alpine.LRH.2.20.1903041505530.3767@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"

Hi Kody

yes, there are some hidden options to recon-all for this. Take a look at
the script for things like -no-cerebellum, -rh-only, and see if they are
sufficient for what you are trying to do

cheers
Bruce