Hey folks,
I am totally new to freesurfer, so please forgive me… I am trying to open up an
atlas in freesurfer that is in 4dfp.ifh format (or nii, if you like). Can
anyone tell me how?
Otherwise, I could try to reconstruct it straight from the T1 anatomical run,
but when I try the following co
To elaborate, the 001.mgz and the orig.mgz have a different number of
voxels and are (generally) sliced differently, so they do not share a
voxel space. The do share an RAS space. The qform (and matrix given by
--vox2ras) is the matrix that converts a voxel coordinates to RAS. This
matrix must
Hi Gabriele,
the 001.mgz is in the original scanner coords, while the orig.mgz has
been "conformed" to be in our standard coronal coordinate system.
cheers
Bruce
On Sat, 22 Jan 2011, Gabriele Arnulfo wrote:
> Hi again I've finally found the exact transformation which is ... gather
> from the
Hi again I've finally found the exact transformation which is ... gather
from the original nifti the qfrom matrix (say Qf) and then collect with
mri_info vox2ras-tkr orig.mgz , the transformation matrix (say T) to map ras
to index in the freesurfer space. I've finally matched the points.
Why mri_i
I don't know of another way to map control points. By MRI space I assume
that you mean the scanner RAS space? Eg, the space defined by the nifti
qform? I think this matrix will be
L = inv(T)*Q
where Q is the scanner vox2ras of the orig volume and T is the
tkregister vox2ras of the orig volume.
Hi Gabriele,
not sure if there is an easy way (probably Doug knows). But if there
isn't, I wrote a tool mri_map_cpdat to map control points from one space
to another. A control points dat file is a txt file containing
coordinates. The tool will be available in 5.1 where it is used to
transfer manu
Hi all,
I'm a new freesurfer user and I've a small question for you all. Which
the faster and reliable way to map a list of points into the freesurfer
geometrical space?
I've already read the pdf/ppt but there's no suggestion in there about
which command should be used (if any). I've read about m
