Hello freesurfer Expert,
Steps for measuring cortical thickness are in tkmedit :
1.
Intensity normalisation,
2.
Registration to Talairach space,
3.
Skull stripping,
4.
Segmentation of white matter,
5.
*Tesselation of the WM boundary, *
6.
*Smoothing of the
Hi all
i am developping an application for neuronavigation, and i want to use
freesurfer cortical parcellation and sub-cortical segmentation, is there any
freesurfer command to convert surface files to vtk files ?
Thanks
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Hi Saurabh
this is all done for you in recon-all (not tkmedit). Why not just run it?
Bruce
On
Mon, 10 Mar 2014, Saurabh Thakur wrote:
> Hello freesurfer Expert,
> Steps for measuring cortical thickness are in tkmedit :
> 1.
>
> Intensity normalisation,
>
> 2.
>
> Registration to Talai
On 03/07/2014 07:46 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks for your reply. Yes there were areas of significant difference
> reported in the age slopes maps, after the mri_glmfit command was run.
> However, I haven't checked to see yet whether there are surviving clusters
> af
We do have a label for transversetemporal. What do you want to do with
it? You can extract it out of ?h.aparc.annot or aparc+aseg.mgz,
depending on what you want to do with it
doug
On 03/08/2014 06:48 AM, Ritobrato Datta wrote:
> Hi All,
>
> I need to demarcate primary auditory cortex in a grou
Do you mean you want to display them in the MRI volume or on the surface
(or both)? When you say that they are in "RAS coordinates", what do you
mean? How are the coords defined?
doug
On 03/08/2014 07:26 AM, peng wrote:
> Dear freesurfers,
>
>I have a set of dot locations (300~400) in a t
No, it was not a problem with negative thickness but an
inaccuracy/inconsistency with the way the surfaces were computed. It is
not something that is easy to notice (which is how it made it past our QA).
I would re-run them.
doug
On 03/08/2014 11:21 PM, Gregory Kirk wrote:
> In the release not
On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
> Hi Doug,
>
> To clarify my previous question:
>
> There is definitely some fuzziness when comparing with the mov,
> whereas the target comparison looks very pristine. I was just
> wondering if this is expected. The mov, as I scroll through the layers
On 03/09/2014 05:24 PM, Tudor Popescu wrote:
> Hello,
>
> In addition to this last question, I'd also like to ask the following:
>
> 1) It's very hard to understand a group X gender interaction (age as
> nuisance) on a graph that has age on the x axis, and with 4 regression
> lines corresponding
Hi All,
My email may have fallen through the cracks over the weekend so I am sending it
again.
I need to demarcate primary auditory cortex in a group of subjects anatomically
and I came across the following papers -
https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_al.
Hi Doug,
Wow, telepathy…Just resent my email and got this reply. THanks. I need to
compute the surface area of primary auditory cortex so was looking for an
approach similar to the Hinds V1 approach and came across two papers by your
group. So if I can demarcate A1 based on myelination patterns
Dear Experts,
I am very new to TRACULA, I apologise for what is probably a silly question.
I've got the following error on running trac-all -prep (FreeSurfer 5.2.0):
awk: cmd. line:1: fatal: cannot open file `0' for reading (No such file or
directory)
mri_concat --i
/home/k1193186/FreeSurfer/T
Our lab has a need to apply the Yeo atlas to individual brains. As I understand
it, Yeo atlas is only currently available for the FSAverage brain. Any plans to
incorporate Yeo on to the default FS segmentation, or have it available as an
option?
-Jeff Eriksen
__
Thanks Doug for your reply. In fact I need both. I do this mainly for
computation (in volume); and display (in surface) is also cool.
The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in volume
of the template (icbm152). This can be implemented as an Nx3 matrix S,
where S(n, :) = [n
Hi Jeff
you should be able to use mri_label2label to map the Yeo atlas from
fsaverage to any subject.
cheers
Bruce
On Mon, 10 Mar 2014, Jeff Eriksen wrote:
Our lab has a need to apply the Yeo atlas to individual brains. As I
understand it, Yeo atlas is only currently available for the FSAve
What I need are the ?h.Yeo.annot files for the individual subjects, similar to
the default ?h.aparc.annot and ?h.aparc.2009.annot files. Will mri_label2labe
give me that directly?
Thanks,
-Jeff
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Monday, Mar
Hi ,
mris_convert has some functionality for VTK output.
Best, Martin
On 03/10/2014 09:51 AM, LAOUCHEDI MAKHLOUF wrote:
Hi all
i am developping an application for neuronavigation, and i
want to use freesurfer cortical parcellation and sub-cortical
segmentation, is there any freesurf
Hi Kaiming,
I'm almost certain you are right at the medial line and what you are
seeing is the transition from one hemi to the other. Most likely the
brain is slightly oblique and so the sagittal slice does not perfectly
bisect the two hemispheres.
-Louis
On Mon, 10 Mar 2014, Kaiming Yin wrote
Hi Jeff,
I am a little unsure myself since I usually work with data mapped to
fsaverage space. I think you might want to use mri_surf2surf, since
there's a "--sval-annot" option. It's hard for me to check now because
I am away at a conference.
Can someone chime in if mri_surf2surf is wrong?
Than
Hi Colm - Note that the information in the tutorial (particularly the part
where gradient tables can be formatted in 3 rows or 3 columns) pertains to
the latest tracula update:
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates
You're using an older version that only supports th
Regarding matlab:
Currently, I have in freesurfer the surface extracted via recon-all. I also
have the overlay from running mri_vol2surf on the ICA components.
I would like to export the pial surface + overlay into matlab together as a
single object. Is there a matlab script for this, or do I
problem with surf2surf is it deals with scalar fields ( data ) so don't think
that will do it.
problem with label2label is that it deals with a single label which has a
diferent structure than anot.
so a way to do it
1. mri_annotation2label ... to convert the yeo anotation file to individual
yes, that is the option. If you run it with --help, it will actually
give you an example.
doug
On 3/10/14 7:23 PM, Thomas Yeo wrote:
> Hi Jeff,
>
> I am a little unsure myself since I usually work with data mapped to
> fsaverage space. I think you might want to use mri_surf2surf, since
> there's
Should also add that I can import the cortical surface into matlab without any
issues using read_surf.m what I would like to have is the ICA overlay also
imported into matlab as corresponding colors for each face on the cortical
mesh. Thanks.
From: andrewz...@live.com.au
To: gr...@nmr.mgh.har
I don't know of anything that will do this (or what a single object
would mean in this case). If you have the overlay in a volume format
(eg, mgz), you can use MRIread.m. This gives you a value for each
vertex, not face, so you'd have to write something to assign the value
to a face.
doug
Hello Freesurfer,
Laplacian based method for measuring Cortical thickness
Can u anyone help me to understand how freesurfer has implemented this algo
and where to find this algo for better understanding.
Thanks,
Saurabh Thakur,
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