Re: [Freesurfer] directional cosine error?

If you have a tkregister registration file called subj1.mat, then name it something else as the volume reading tools think that is an spm-style .mat file and try to read it as a matlab4 matrix.

doug

Nguyen, Thang Q wrote:

Hello all,

I get a directional cosine error when I try to register data or extract values from them so I tried mri_info and get this message:

mri_info subj1.img

matfile: only read 256 bytes of name (810698068 specified)

MatlabRead: readHeader returned NULL

WARNING: analyzeRead(): matfile subj1.mat exists but could not read ...

may not be matlab4 mat file ... proceeding without it.

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INFO: could not find subj1.mat file for direction cosine info.

INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).

INFO: if not valid, please provide the information in subj1.mat file

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Volume information for subj1.img

      type: analyze4d

dimensions: 79 x 95 x 68

voxel sizes: 2.0000, 2.0000, 2.0000

      type: FLOAT (3)

       fov: 79.000

    xstart: -39.5, xend: 39.5

    ystart: -47.5, yend: 47.5

    zstart: -34.0, zend: 34.0

        TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 

0.00 degrees

   nframes: 1

ras xform present

xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r 

= 0.0000

          : x_a =   0.0000, y_a =   1.0000, z_a =   0.0000, c_a 

= 0.0000

          : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s 

= 0.0000

Orientation : LAS

Primary Slice Direction: axial

voxel to ras transform:

           -2.0000   0.0000   0.0000    79.0000

            0.0000   2.0000   0.0000   -95.0000

            0.0000   0.0000   2.0000   -68.0000

            0.0000   0.0000   0.0000     1.0000

voxel-to-ras determinant -8

ras to voxel transform:

           -0.5000  -0.0000  -0.0000    39.5000

            0.0000   0.5000   0.0000    47.5000

            0.0000   0.0000   0.5000    34.0000

            0.0000   0.0000   0.0000     1.0000

Here is the mat file:

Subj1

2.000000

2.000000

200.000000

1.054861e+00 -2.348376e-02 -1.086195e-01 7.747378e-01

9.350572e-02 -3.302234e-01 1.067427e+00 -3.124532e+01

-4.640190e-02 -9.299399e-01 -3.056859e-01 -7.546637e+00

0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00

round

What does the matlab error mean? Why can't it read the directional cosine?

-Thang

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