Dear Freesurfer Experts,
I'm trying to convert .label file to .stl file.
In more detail of my purpose, I want to get separate stl files of whole brain.
Now, I want to make stl files of label files which made from
?h.aparc.a2009s.annot.
First, I tried to convert lh.pial to lh.pial.stl, I've
The Molecular Imaging and Neuropathology Division at Columbia University
Medical Center is seeking a full-time image analyst to begin working
immediately. The position involves assisting in the processing of brain imaging
data, including positron emission tomography (PET) and structural and
Hi Qijing,
Under the 'Freeview dev build' section on this wiki page you can download
an updated version of freeview.
http://freesurfer.net/fswiki/Download
-Louis
On Mon, 7 Jul 2014, Qijing Yu wrote:
Hi Doug,
By new version, do you mean v5.3.0?
Qijing
On Mon, Jul 7, 2014 at 11:31
Hi Bruce,
Thanks for your reply. In my previous e-mail I already tried to attach one of
my subjects, but got the response that the message was too big, and therefore
it was rejected. So how should I upload the image? The images are T1-weighted,
3D, acquired with a 3T scanner, resolution 256
It probably thinks the STL file is just a mesh without coloring.
Peace,
Matt.
From: Mat yuki matsuyuki2...@outlook.jp
Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Date: Thursday, July 10, 2014 at 7:19 AM
To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu
Hi Doety,
Consider these options for uploading data:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
I think recon-all is expecting your wm.mgz to be conformed or 256^3.
Something like: mri_convert wm.mgz wm.conform.mgz
If you have matlab, it would be pretty easy to do it there, something like
aseg = MRIread('aseg.mgz');
seg = MRIread('seg_edited.mgz');
% Your first seg inside cerebellum
indseg1 = find(seg.vol == 1 (aseg.vol == 8 | aseg.vol == 47));
% cerebellum cortex = 8 and 47, see
I don't think you need to do steps 2 and 3. Just run
mri_annotomical_stats on the lobes annot just like it is done for aparc.
Look in the recon-all.log file for the command line
doug
On 07/08/2014 02:42 PM, krista kelly wrote:
Hi all,
I'm trying to extract cortical thickness data from each
This is expected, unfortunately. When you change the orientation, it
changes the interpolation which changes things slightly. Those areas are
all pretty small so the changes can appear to be large (though they are
only a few percent).
doug
On 07/09/2014 01:42 PM, Kathy L. Pearson wrote:
I
You cannot use qdec for this. You must use the command line stream.
There is a tutorial for this as well as a presentation on our wiki.
Basically, you will need to create your FSGD file, run mris_preproc,
mri_surf2surf to smooth, mri_glmfit, and mri_glmfit-sim
doug
On 07/09/2014 03:43 AM,
Hi Andre
You can run:
mri_jacobian -tm3d 3d morph template volume output volume
--Lilla
On Thu, 10 Jul 2014, André Ribeiro wrote:
Dear Freesurfer Community,
How can I obtain the Jacobian of the deformation field estimated through
mri_cvs_register for further use like VBM analysis?
Dear Freesurfer Community,
How can I obtain the Jacobian of the deformation field estimated through
mri_cvs_register for further use like VBM analysis?
Regards,
Andre Santos Ribeiro
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Thank you Doug and Louis!! was stuck in something else in the past few
days. I will try the new version and let you know if I still have problems
viewing the results.
Thanks again! Really appreciate your help!
On Thu, Jul 10, 2014 at 10:57 AM, Louis Nicholas Vinke
vi...@nmr.mgh.harvard.edu
Thank you Douglas for the suggestion, I will try this method!
Alexarae
On Thu, Jul 10, 2014 at 11:43 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
If you have matlab, it would be pretty easy to do it there, something like
aseg = MRIread('aseg.mgz');
seg =
Hi FS Community,
I was wondering whether LGI and Surface Area need to be corrected for
total Intracranial Volume.
Thanks in advance,
Panos
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Hi Panos,
It all depends on what your question is: whether the between-group difference
in LGI and surface area is an absolute difference (then don't correct), or
whether you want to see if it holds after correction. In any case, by geometric
definition, the relationship between surface area,
Hi Marie,
Thank you for your reply. I wanted to compare the LGI and Surface Area
between two cohorts, from which one has a significantly higher
intracranial volume than the other. I was wondering about the correction
because the results, especially in the case of SA, are the opposite before
and
Hi,
Freesurfer reported the following hippocampal volumes for a subject
volumeInVoxels:
right_CA1: 2652.3
right_CA2_3: 7245.11
right_CA4_DG: 3967.28
right_fimbria: 423.555
right_hippocampal_fissure: 191.897
right_presubiculum: 3598.99
right_subiculum: 4868.1
Hello,
I have a few questions about Tracula. I am very new to DTI, so I hope you can
bare with me.
1.) I have been checking my registration at the prep stage. I am very new to
this so it may be that I am not looking at the right files.
I looked at my eddy current corrected diffusion data
Hi Panos,
Then I would say that it's interesting to understand why the results change
depending on the correction. Here is a list of papers that may be relevant, but
you'll certainly find many others:
http://www.ncbi.nlm.nih.gov/pubmed/8159014
http://pages.jh.edu/~kechen/pnas-brains.pdf
For surface area, you should correct with the ICV (note you should use
ICV and not something like ICV^(2/3))
doug
On 07/10/2014 04:52 PM, Marie Schaer wrote:
Hi Panos,
Then I would say that it's interesting to understand why the results change
depending on the correction. Here is a list
Hello Freesurfer experts:
I am wondering if I can do ACPC alignment in freeview. Perhaps using Tools
Transform volume and then rotating using landmarks.
Is this indeed possible? If so, can anyone provide guidance on the 3 landmarks
to select (would it be anterior commissure superior posterior
Hi Matt,
Thank you for your reply. It is impossible to convert label file to stl file,
is it wright?
If it was so, do you know how to get it? I want to get stl files which divided
into each percellation, if its possible.
Thanks in advance,
Yuki.
Date: Thu, 10 Jul 2014 10:25:19 -0500
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