Great. Sorry, I'm a but slow on the uptake sometimes :)
Thanks for your help!
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 9/9/2005 9:46 AM
To: Fornito, Alexander
Cc: Doug Greve; freesurfer@nmr.mgh.harvard.edu
no, I mean just rerun all the automated steps, and retain your old edits.
On
Fri, 9 Sep 2005, Fornito, Alexander wrote:
Sorry, when you say "safest thing to do is to rerun everything " do you mean
including doing the manual edits again?
I'm doing strcutural studies, so I want to make sure I
Sorry, when you say "safest thing to do is to rerun everything " do you mean
including doing the manual edits again?
I'm doing strcutural studies, so I want to make sure I get it right!
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 9/9
it's no faster on the re-run (unfortunately)
Fornito, Alexander wrote:
I understand. Good to hear I wouldn't have to do all the manual editing again.
Would it still take about 24 hours from start to finish, or is much quicker on
the re-run?
-Original Message-
From: Bruce Fischl
probably. The safest thing to do is to rerun everything to make sure that
all your subjects were processed in the same way. This probably isn't so
important for functional studies, but can be for structural.
On Fri, 9 Sep 2005, Fornito, Alexander wrote:
I understand. Good to hear I wouldn't h
I understand. Good to hear I wouldn't have to do all the manual editing again.
Would it still take about 24 hours from start to finish, or is much quicker on
the re-run?
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Fri 9/9/2005 9:31 AM
we just have to test it. We've run the equivalent process many times,
just not in the recon-all env yet.
On Fri, 9 Sep 2005, Fornito, Alexander
wrote:
Do you mean you're not sure if it will work?
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
S
Do you mean you're not sure if it will work?
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 9/9/2005 9:28 AM
To: Fornito, Alexander
Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Intst
You should be able to run it with -autorecon-all -rerun. Having said
that, I don't know that we've actually run it that way.
doug
Fornito, Alexander wrote:
Hi Bruce and Doug,
When you say it can be done automatically,does that mean it wouldn't require additional editing? Does it use edit
yes, it will keep any existing edits or control points.
On Fri, 9 Sep 2005,
Fornito, Alexander wrote:
Hi Bruce and Doug,
When you say it can be done automatically,does that mean it wouldn't require
additional editing? Does it use edits that are already performed (eg., in
creating surfaces w
Hi Bruce and Doug,
When you say it can be done automatically,does that mean it wouldn't require
additional editing? Does it use edits that are already performed (eg., in
creating surfaces with the dev version)?
If so, do you know how long it would roughly take to re-create them in this
way?
Tha
I am having some trouble running recon-all.
one thing I have observed:
Freesurfer keeps searching in the /mri folder instead of the /mri/orig folder,
for example, in order to run tkmedit I had to type the command as follows:
tkmedit 2332 orig/orig.mgz
and I had to copy the orig.mgz file from t
Hi all,
is there anyway to change space of the images from 256 x 256 x 256 (in my case in minc format) to output to 172 x 220 x 156?
Thanks!
Tracy Wang
Tracy Wang
Research Assistant
Cognitive Neuroscience Laboratory
Washington University
Department of Psychology, Campus Box 1125
One Brookings D
Hi Keyma,
the new stream fills the entire ventricular system and all the basal
ganglia.
Bruce
On Thu, 8 Sep 2005, Keyma Prince wrote:
Hello,
I tried running one of my subjects through the whole autorecon stream and
I noticed more of the basal ganglia region was filled in then was described
Hello,
I tried running one of my subjects through the whole autorecon stream and
I noticed more of the basal ganglia region was filled in then was described
in the previous tutorial. Is this extra filling ok? The data I ran it on
is located in /space/engram/11/users/rk_fmri_struc/Y24_010705a_STRUC
the subcortical segmentation (Neuron paper) is included in it.
cheers,
Bruce
On Thu, 8 Sep 2005, Stephanie McMains wrote:
Are there other new scripts or features in the dev release other than the
recon-all stuff?
Thanks,
Stephanie McMains
On Sep 8, 2005, at 10:09 AM, Nick Schmansky wrote:
Are there other new scripts or features in the dev release other than
the recon-all stuff?
Thanks,
Stephanie McMains
On Sep 8, 2005, at 10:09 AM, Nick Schmansky wrote:
A new set of Linux 'dev' distributions has been uploaded which
contain the recon-all bug fix. That link is:
https://surfe
A new set of Linux 'dev' distributions has been uploaded which
contain the recon-all bug fix. That link is:
https://surfer.nmr.mgh.harvard.edu/pub/dist/?M=D
You can either get that new distribution, or just copy the recon-all
taken from Doug's link below to your $FREESURFER_HOME/bin directory.
Hi Alex,
you probably want to regenerate everything. Note that this can be done
automatically through recon-all (Doug can tell you the switches).
cheers,
Bruce
On Thu, 8 Sep 2005, Fornito, Alexander wrote:
Seems to be working now. Thanks Doug, you're a lifesaver!!
As an aside, will surfac
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