Hi Doug and list,
I'm trying to map surface/mesh vertices (e.g. rh.pial) to voxels
(cols, rows, slices) in a functional volume in matlab,
and just wanted to a) get a check that what I'm doing sounds right and
b) share it in case it's useful to anyone else
(I searched the mailing list and found most
Hi Pom
ry removing the lines that say:
#---CUT HERE---
cheers
Bruce
On Thu, 10 Feb 2011, Pom Sailasuta
wrote:
> Hello,
>
> I just installed freesurfer on my new Fedora 14 desktop following the
> instruction from the
> website. Howver when testing for installation, ther
Hello,
I just installed freesurfer on my new Fedora 14 desktop following the
instruction from the
website. Howver when testing for installation, there are errors as follows:
[root@pom-PC stable5]# tkmedit bert orig.mgz
--
ERR
Hi Scott
we don't usually recommend having any voxel dimension > 1.5mm, and
try to be closer to 1mm iso. I'm surprised that your results have been
positive so far. I doubt the thickness estimates will be terribly
sensitive, but there's nothing but compute time to be lost by trying.
cheers
Bruc
Hi All,
Is the following T1 sequence suitable for surface generation?
"T1-weighted 3D SPGR (echo time 5 minimum; repetition time = 24 msec; flip
angle
= 30; field of view = 24 centimeters; slice thickness = 3 millimeters)
collected
in the axial plane."
It's that 3 mm slice thickness that mos
Dear All,
I was wondering if anyone knows of a step-by-step guide on how to do
retinotopic analysis with freesurfer.
Thanks.
Michelle
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Hi Yolanda,
the first command maps the aseg from the "conformed" voxel geometry back to
the voxel geometry on the scanner, and the second extracts the caudate from
that volume. If you want the caudate in the conformed space, just use
aseg.mgz in the mri_extract_label command instead of aseg-in
Dear freesurfer's,
I have run a conventional recon-all process and I am interested in isolating
the caudate from my subjects. I have applied the following commands:
*./mri_label2vol --seg $SUBJECTS_DIR/$subj/mri/aseg.mgz --temp
$SUBJECTS_DIR/$subj/mri/rawavg.mgz --o
$SUBJECTS_DIR/$subj/mri/aseg-i
Hi Jason
you can't get all the voxels onto the surface, as the surface is a 2D
sheet cutting through a 3D volume. This is actually one of the big
advantages of surface-based analysis as you avoid most of the regions
that shouldn't have signal (e.g. ventricles, white matter, etc...). That
said,
RhFFA_sphere.label when loaded on functional data seems to correspond
to RhFFA_sphere.nii.gz when loaded on anatomical data. When the label
is just loaded on the nii.gz file, they seem to overlap, but if they
are both overlaid on an anatomical image, the label is far superior to
the nii.gz mask.
A
Dear Doug,
Thank you! I was able to display on the freesurfer surface from a matlab array
to surface pipeline.
However, only a portion of my voxels showed up on the surface, presumable owing
that the others fall in the white matter ...
My question is: is there any way to override this so that
Thank you for your advice Doug.
Best wishes,
-jason.
>-Original Message-
>From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
>Sent: 09 February 2011 16:42
>To: Jason Connolly
>Cc: 'freesurfer@nmr.mgh.harvard.edu'
>Subject: Re: [Freesurfer] phase data overlay using fsaverage
>
>Fir
Dear doug,
Thank you for your quick reply - Unfortunately this does not yet work. I
have written a small matlab example to more clearly show my problem:
clear all; clc;
% I would like to load a surface with
% [rh.pial.vertices,rh.pial.faces] = read_surf([surfdir 'rh.pial' ]);
%
% rh.pial.vertice
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