Hi all,
I have one problem about rending ROI from VBM onto Freesurfer average surface
and extracting thickness in this ROI region. I have already extracted one
cluster (my ROI ) from VBM_derived group difference t_statistic map.
I got a lot of information from this mail list, especially Alex's
Hi Li,
there you go,
Gari
https://docs.google.com/open?id=0Byf71TWfovledFhJYWN2cGtHV00
On 2012-09-15, at 19:38, "Kong, Li" wrote:
> Hi Gari,
> I saw your email to Alex about your method obtaining statistics from multiple
> subjects with Python script. Could you send the code to me?
>
> Th
Does anyone have any suggestions on what might have gone wrong here? Should
I send the image?
On Fri, Sep 14, 2012 at 3:14 PM, Blessy M wrote:
> No, the cerebellum is not attached.
>
> On Fri, Sep 14, 2012 at 1:42 PM, Blessy M wrote:
>
>> I have a MPRAGE scan, with slight atrophy on right side
that is a pretty big defect (vertices=27939). Can you check the
?h.orig.nofix and see if anything is dramatically wrong with it? Is the
skull attached? The cerebellum? If you upload it we can certainly take a
look
cheers
Bruce
On Mon, 17 Sep 2012, Blessy M wrote:
Does anyone have any suggest
Hi Harry
what system and shell are you running on?
cheers
Bruce
On Mon, 17 Sep 2012,
hhal5...@uni.sydney.edu.au wrote:
> Hello,
>
> I am relatively new to FreeSurfer, so this may be a silly question, but when
> i run any of the recon-all commands such as:
>
> recon-all -autorecon-pial -subjid
Yes, just add --trgsubject fsaverage
doug
On 09/15/2012 07:02 PM, Maryam Vaziri Pashkam wrote:
> Hi Doug,
>
> This is a separate question but related to the volume to surface
> conversion. Is it possible to sample the sig.nii.gz file to the
> fsaverage surface instead of the individual subject
Hi Li, as suggested by Voet, the best way to do it will be to map the
VBM results back to the individual subject. Unfortunately, this is an
FSL operation, so you should contact the FSL list as to how to do this.
doug
On 09/17/2012 06:37 AM, Kong, Li wrote:
>
> Hi all,
>
> I have one problem abou
Hi Doug,
Thanks for your idea! I will try FSL.
Li
-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve
Gesendet: 17 September 2012 16:06
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Free
Good news, I recreated the FSGD file from scratch on a linux workstation
using the exact same syntax and list of inputs and re-ran the mri_preproc
and it worked this time. The original file that I was having issues with
was also created on a linux workstation, however I had copied the inputs
from a
Hi everyone,
We have run FreeSurfer on roughly 60 subjects for a study, and are
noticing some strange discrepancies for intracranial volume in
aseg.stats for 8 of them. Here is a subset of what we see in one of the
"bad" aseg.stats files:
# Measure CorticalWhiteMatter, CorticalWhiteMatterVol,
Hi Nikhil,
this indicates a problem with the talairach.xfm computation. The ICV is
computed from the Talairach transform (which basically determines how
much stretching is needed to get this image to the talairach space where
the ICV is approx known). There is no mask.
See
http://www.freesurfer.
I'm still trying to figure out a way to display an ROI made elsewhere on my
freesurfer data. I can get all ROI I need in freesurfer in talairach
points (ie. a list of talairach points that cover the entirety of the ROI
space), but as far as I can see, I can only load one talairach point at a
time
Hi Katie
you might be able to create a label file with the tal coords, then use
mri_label2label to map it from tal to the individual subject, then load it
in tksurfer which will map it to the surface. It will probably look spotty
though.
cheers
Bruce
On Mon, 17 Sep 2012, Katie Bettencourt
Hi all,
I'm new to FreeSurfer and so have a few questions that you may be able to
anwser.
My first question is ; when I am making white matter edits do I need to
edit every single slice where the inaccuracy is or would every second or
third slice suffice to prompt FreeSurfer to autocorrect?
Seco
Hi Bruce,
So my understanding of the label file is that it has a list of the # of
vertices in the label, then each line is the vertex number followed by the
RAS coordinates and then some 5th column. I think you are saying that I
could use my text file of talairach coordinates (with each line as a
Hi Katie
if you set the vertex numbers to -1 then tksurfer will search for the
closest vertex to each point and fill them in. So start with a list of
tal points (and -1 for the vertex), then use mri_label2label to map them to
the individual subject space and visualize it in tkmedit or freeview
I think mri_label2label will do the same thing
On 09/17/2012 01:25 PM, Bruce Fischl wrote:
> Hi Katie
>
> if you set the vertex numbers to -1 then tksurfer will search for the
> closest vertex to each point and fill them in. So start with a list of
> tal points (and -1 for the vertex), then use
-- Forwarded message --
From: Richard Binney
Date: Thu, Sep 13, 2012 at 2:01 PM
Subject: Freeview display errors - Ubuntu 12.04
To: freesurfer@nmr.mgh.harvard.edu
Hi Freesurfers,
I've recently moved onto Ubuntu 12.04. The Freesurfer installation has
required me to download vario
So the left side has gone all the way through, and "lh.volume" was created,
but it looks like the right side has some files missing.
Can I just upload the raw data file? Should I attach it in my email?
On Mon, Sep 17, 2012 at 9:40 AM, Bruce Fischl wrote:
> that is a pretty big defect (vertices=2
you can ftp it
Bruce
On Mon, 17 Sep 2012, Blessy M wrote:
So the left side has gone all the way through, and "lh.volume" was created,
but it looks like the right side has some files missing.
Can I just upload the raw data file? Should I attach it in my email?
On Mon, Sep 17, 2012 at 9:40 AM, B
Hi Bruce,
I am running on Linux-centos4-stable-pub-v5.1.0 and using bash. Though I have
tried using csh and tcsh, but the same error comes up.
Cheers,
Harry
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf
Also we're using ubuntu 12.04 LTS.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
hhal5...@uni.sydney.edu.au [hhal5...@uni.sydney.edu.au]
Sent: Tuesday, 18 September 2012 10:54 AM
To: Bruce Fischl
Cc: fre
Hello,
After running -autorecon1, there were issues with finding the best water
threshold for skull stripping (one value would leave excess anatomy and the
next lowest value would leave regions in the cerebellum missing).
FS appears to differentiate brain matter from extraneous anatomy quite w
Definitely the one that leaves stuff around and doesn't strip any brain.
Usually that won't be a problem
Bruce
On Sep 17, 2012, at 10:20 PM, Skyler Gabriel Shollenbarger
wrote:
> Hello,
>
> After running -autorecon1, there were issues with finding the best water
> threshold for skull strip
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