Hi Deirdre
just copy the updated recon-all into $FREESURFER_HOME/bin and you should
be all set
cheers
Bruce
On Mon, 17 Dec 2012, Deirdre O Shea wrote:
Hi,
I have experienced this problem before also.So I have downloaded the script you
provided but as a non-programmer I am wondering
how I can incorporate this script into my work using Linux. Can I simply copy
and paste this into the text editer and run it
that way?
Thanks,
Deirdre
On Fri, Dec 14, 2012 at 4:37 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
it doesn't, although the 5.2 mri_normalize should help as well
cheers
Bruce
On Fri, 14 Dec 2012, Jonathan Holt wrote:
OK this is great. Does this require the latest version of
Freesurfer? I see
recon-all v 5.2, we're running Freesurfer 5.0.0 for reference
On Dec 14, 2012, at 1:16 PM, Alex Hanganu wrote:
I think Emily is talking about this one:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/
a.
Le 14/12/2012 12:59 PM, Jonathan Holt a écrit :
Emily,
This is good news, can I find or download this revised version
somewhere?
jon
On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote:
We ran into this issue frequently and found that it
was resolved by using the revised recon -all script
that alters the stage where control points are
considered.
Emily
On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt
<whats...@umich.edu> wrote:
OK will do... I'll upload both versions,
before and after recon-all ran. I am
beginning to think it's an issue with
the script that I am running... I'm
looking at another brain and there are
areas I did not touch at all where white
matter voxels are being added or
removed...
On Dec 12, 2012, at 11:33 AM, Bruce
Fischl wrote:
> Hi Jon
>
> if you upload this subject we'll take
a look
> Bruce
>
>
> On Wed, 12 Dec 2012, Jonathan Holt
wrote:
>
>> I've had this happen a handful of
times and I'm wondering what I can do
about it. For reference using Freesurfer
5.0.0.
>>
>> Edited a brain and ran "recon-all
-autorecon2 -autorecon3 -s subj_id"
which completed without error. The
resulting brain had chunks of missing
auxiliary volume in areas that I had not
touched at all. This is bizarre and I am
not sure what to do about it. Images of
said issue attached of both main and
auxiliary volumes.
>>
>>
>
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