Hi Bruce,
I had tried to run recon-all on the dicoms. But the same errors show up.
This image covering whole brain is obtained (Siemens 3T) actually from a
monkey and looks good. Here is the header information from the dicom image.
According to the suggestion in Freesurfer FAQ, I run "tkregister2
Hi Dhinakaran,
4 and 5 aren't part of our current automated segmentation. Sorry, I'm not
sure how visible they are in a 1mm T1-weighted image
Bruce
On Wed, 17 Nov 2010,
Dhinakaran Chinappen wrote:
> Dear all,
>
> Hope your research is going smoothly.
>
> My question refers to the basal ganglai
can you try running recon-all directly on the dicoms? Also, it's probably
pretty
noisy at .5mm in-plane - how does it look? Is it whole brain?
On Wed, 17 Nov
2010, liang wang wrote:
> Hi Bruce,
>
> I run the command on a NIFTI image converted by dicom files. The image can
> be skull stripped u
It looks like AD8/00275571/surf/lh.sphere.reg may be corrupted. Can you
load it in tksurfer? Is the disk full?
doug
t...@ms36.hinet.net wrote:
>
> Dear FS experts,
>
> I read the tutorial and don't know how to perform average all
> subjects' volume and surface by make_average_subject. I finish a
Dear all,
Hope your research is going smoothly.
My question refers to the basal ganglai components. I previously shot an
email which Prof. Fischl was kind enough to reply to: the basal ganglia is
not computed as a structure of its own in FreeSurfer.
These are the structures of the basal ganglia
Hi Bruce,
I run the command on a NIFTI image converted by dicom files. The image can
be skull stripped using bet in FSL, but some skulls were not removed
clearly. Here is the information by mri_info. It seems to me normal, but
several scan parameters loss. For the nifti image, I use to3d (AFNI cod
Do you have matlab? If so, you can
lbl = read_label('','file.label');
index = lbl(:,1) + 1; % make one-based
thickness = read_curv('lh.thickness');
% These are the values you want:
thicknesslbl = thickness(index);
doug
Sasa Kivisaari wrote:
> Hi all,
>
> Is there a way of ouputting all the thic
wow, that's a completely wacky talairach xform. Did you run this straight
on the dicom images? The talairach clearly failed for some reason. Try
running mri_info on the dicoms to see if there is something strange in
them
On Wed, 17 Nov 2010, liang
wang wrote:
> Hi FSusers,
>
> The terminal di
Hi FSusers,
The terminal displays errors when I run "recon-all -autorecon1 -subjid ..."
to get a skull-stripped brain image. The processing exits with the following
errors regarding talairach transformation. Here is the talairach.xfm:
MNI Transform File
% tkregister2
Transform_Type = Linear;
Lin
It's in the 'dev' tree. You'll have to source the nmr-dev environment
On 11/17/10 10:24 , Marco Loggia wrote:
> Thanks Rudolph.
>
> I don't seem to have that command in my path... I take it is not in the
> standard FreeSurfer distribution (version 5) available here at MGH.
>
> Where do I find it?
Thanks Rudolph.
I don't seem to have that command in my path... I take it is not in the
standard FreeSurfer distribution (version 5) available here at MGH.
Where do I find it?
Thanks,
Marco
-Original Message-
From: Rudolph Pienaar [mailto:rudo...@nmr.mgh.harvard.edu]
Sent: Wednesday,
Dear FS experts,
I read the tutorial and don't know how to perform average all subjects' volume and surface by make_average_subject. I finish all subjects' recon-all steps and try to average them. when I type make_average_subjects --fsgd and it comes out the error message:
$Id: make_average_surface
Try using 'mris_decimate_gui' -- if you pass it a --decimationLevel of
1.00, you can view the surface (un-decimated) and add tweak the "Up
Vector" and "Position" to move the viewpoint.
Look at 'mris_decimate_gui -h' for more options. You can also on startup
specify a view rotation.
HTH
-=R
O
Unfortunately no. I'll put that on my list and target it for the next
release.
On 11/17/10 9:42 AM, Marco Loggia wrote:
Dear all,
I am trying to use the 3D view in freeview to prepare some figures,
and would like to be able to rotate the volume along one axis only
(e.g., yaw).
Is there a
Dear all,
I am trying to use the 3D view in freeview to prepare some figures, and
would like to be able to rotate the volume along one axis only (e.g., yaw).
Is there a way to constrain the rotation with the mouse, and/or to enter the
numerical value of parameters such as azimuth and eleva
Hi all,
Is there a way of ouputting all the thickness values (vertex by
vertex) within a specified label? I would like to get some more
information out of my labels than is provided by mris_anatomical_stats.
All the best,
Sasa
___
Freesurfer mailin
Hi FreeSurfers,
I am converting the pial surface (?h.pial) into STL format and importing it
into Blender as described in
http://surfer.nmr.mgh.harvard.edu/fswiki/BlenderModel. However, I would like
to end up with a render of the whole brain (i.e. including both hemispheres,
cerebellum, brainstem,
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