[Freesurfer] MRIread generating one dimensional vector
I tried using MRIread to look at the contents of the analysis files (using
Fressurfer 5.2.0 under OS X 10.8.3 and Matlab 2013a):
mri = MRIread('ces.nii.gz',0);
but I'm getting one-dimensional vectors:
mri
mri =
srcbext: ''
analyzehdr: []
bhdr: []
vol: [1x163842 double]
niftihdr: [1x1 struct]
fspec: 'ces.nii.gz'
pwd: '/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/CS-v-OTHERS'
flip_angle: 0
tr: 2000
te: 0
ti: 0
vox2ras0: [4x4 double]
volsize: [1 163842 1]
height: 1
width: 163842
depth: 1
nframes: 1
vox2ras: [4x4 double]
nvoxels: 163842
xsize: 1.
ysize: 1.
zsize: 1.
x_r: -0.
x_a: 0.0067
x_s: -0.0150
y_r: 4.1714e-08
y_a: 0.9131
y_s: 0.4078
z_r: -0.0164
z_a: -0.4077
z_s: 0.9130
c_r: -6.8259e+04
c_a: 465.0319
c_s: -995.9002
vox2ras1: [4x4 double]
Mdc: [3x3 double]
volres: [1. 1. 1.]
tkrvox2ras: [4x4 double]
It's fine when I read one of the functional files (f.nii.gz).
Am I doing something wrong? Or if it is supposed to be like this, how do I
convert to XYZ coordinates? The vox2ras fields are expecting a
four-dimensional matrix.
Thanks!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
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Re: [Freesurfer] MRIread generating one dimensional vector
That is a surface file. Each of the 163842 values corresponds to a
vertex in the surface. If you want xyz, you need to load in the surface.
You can also analyze the data in the native space if that would make it
easier (but you can't surface smooth).
doug
On 05/30/2013 05:08 PM, Joseph Dien wrote:
I tried using MRIread to look at the contents of the analysis files
(using Fressurfer 5.2.0 under OS X 10.8.3 and Matlab 2013a):
mri = MRIread('ces.nii.gz',0);
but I'm getting one-dimensional vectors:
mri
mri =
srcbext: ''
analyzehdr: []
bhdr: []
vol: [1x163842 double]
niftihdr: [1x1 struct]
fspec: 'ces.nii.gz'
pwd: '/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/CS-v-OTHERS'
flip_angle: 0
tr: 2000
te: 0
ti: 0
vox2ras0: [4x4 double]
volsize: [1 163842 1]
height: 1
width: 163842
depth: 1
nframes: 1
vox2ras: [4x4 double]
nvoxels: 163842
xsize: 1.
ysize: 1.
zsize: 1.
x_r: -0.
x_a: 0.0067
x_s: -0.0150
y_r: 4.1714e-08
y_a: 0.9131
y_s: 0.4078
z_r: -0.0164
z_a: -0.4077
z_s: 0.9130
c_r: -6.8259e+04
c_a: 465.0319
c_s: -995.9002
vox2ras1: [4x4 double]
Mdc: [3x3 double]
volres: [1. 1. 1.]
tkrvox2ras: [4x4 double]
It's fine when I read one of the functional files (f.nii.gz).
Am I doing something wrong? Or if it is supposed to be like this, how
do I convert to XYZ coordinates? The vox2ras fields are expecting a
four-dimensional matrix.
Thanks!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com mailto:jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] MRIread generating one dimensional vector
Oh duh. Okay, thanks!
Joe
On May 30, 2013, at 5:38 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
That is a surface file. Each of the 163842 values corresponds to a vertex in
the surface. If you want xyz, you need to load in the surface. You can also
analyze the data in the native space if that would make it easier (but you
can't surface smooth).
doug
On 05/30/2013 05:08 PM, Joseph Dien wrote:
I tried using MRIread to look at the contents of the analysis files (using
Fressurfer 5.2.0 under OS X 10.8.3 and Matlab 2013a):
mri = MRIread('ces.nii.gz',0);
but I'm getting one-dimensional vectors:
mri
mri =
srcbext: ''
analyzehdr: []
bhdr: []
vol: [1x163842 double]
niftihdr: [1x1 struct]
fspec: 'ces.nii.gz'
pwd: '/Volumes/Data/CP1/fsfast/CPA003/bold/CPA.sm05.lh/CS-v-OTHERS'
flip_angle: 0
tr: 2000
te: 0
ti: 0
vox2ras0: [4x4 double]
volsize: [1 163842 1]
height: 1
width: 163842
depth: 1
nframes: 1
vox2ras: [4x4 double]
nvoxels: 163842
xsize: 1.
ysize: 1.
zsize: 1.
x_r: -0.
x_a: 0.0067
x_s: -0.0150
y_r: 4.1714e-08
y_a: 0.9131
y_s: 0.4078
z_r: -0.0164
z_a: -0.4077
z_s: 0.9130
c_r: -6.8259e+04
c_a: 465.0319
c_s: -995.9002
vox2ras1: [4x4 double]
Mdc: [3x3 double]
volres: [1. 1. 1.]
tkrvox2ras: [4x4 double]
It's fine when I read one of the functional files (f.nii.gz).
Am I doing something wrong? Or if it is supposed to be like this, how do I
convert to XYZ coordinates? The vox2ras fields are expecting a
four-dimensional matrix.
Thanks!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com mailto:jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine
at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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