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: 1.0000
>> ysize: 1.0000
>> zsize: 1.0000
>> x_r: -0.9999
>> 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: [1.0000 1.0000 1.0000]
>> 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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--------------------------------------------------------------------------------
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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