[VoxBo] Reading voxbo files (cub tes res) in Matlab

[Joonkoo Park]

Thanks a lot!
It surely does get me started.

Joon

On Nov 15, 2007 3:51 PM, Daniel Drucker <ddrucker at psych.upenn.edu> wrote:

> > Is there an easy way to read voxbo files (e.g. cub, tes, res, etc.) from
> > matlab?
>
> This is really, really inefficient, but this does the trick for me.
> Note that you must have the SPM toolkit installed, and that you might
> run into endian-ness issues. (If you fix those, please share your
> solution back to me!)
>
>
> function cub = readcub(cubfile)
> % cub = readcub(filename)
> % Extremely inefficiently reads a VoxBo cub as a 3D matrix.
> % Inefficiently, because it uses SPM's spm_read_vols, which only deals
> with
> % hdr/img format; thus, we actually shell out to VoxBo to convert the cub
> % to that format, read, then delete the temp file we read.
> %
> % this function is smart enough to just read the img if passed a filename
> % ending in img
> %
> % WARNING, this has endian-ness problems
> %
> % 2007 ddrucker at psych.upenn.edu
>
> warning off; % quiet SPM's warning about flips
> if strcmp('.img',cubfile(end-3:end))
>    cub=spm_read_vols(spm_vol(cubfile));
> else
>    tmp = num2str(ceil(1E8*rand));
>    system(['vb2img ' cubfile ' /tmp/' tmp '.img > /dev/null']);
>    cub=spm_read_vols(spm_vol(['/tmp/' tmp '.img']));
>    delete (['/tmp/' tmp '.img']);
>    delete (['/tmp/' tmp '.hdr']);
> end
> warning on;
>
>
>
>
> Here's something to write cubs, but I'm even less happy with this
> code, and would greatly welcome comments from someone who understands
> how the affine transformation matrix is supposed to go.
>
> function writecub(filename,volume,datatype)
> % WRITECUB(FILENAME,VOLUME) writes a functional cub.
> % WARNING, this has endian-ness problems
> %
> % 2007 ddrucker at psych.upenn.edu
>
> warning off; % ignoring the flipped warning
> if nargin<3
>    datatype=16384; % double swapped
> end
> if nargin==3 && strcmp(datatype,'mask')
>    datatype=1024;
> end
>
> v.fname=[filename '.img'];
> v.dim=[size(volume) datatype];
> v.mat=eye(4,4); % not really sure if this is right
>                % i might be supposed to say the 3x3x3 if it's a functional
>
> spm_write_vol(v,volume);
> system(['vb2cub ' filename '.hdr ' filename '.cub > /dev/null']);
> delete([filename '.hdr']);
> delete([filename '.img']);
> warning on;
>
>
>
> Anyway, this might help you get started.
>
> Daniel Drucker
>
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