nirs2img, create an image file from NIRS data

51 sec read

Update 2021/2/27: If you find griddata3 not working, try to change griddata3 to griddata.

I was asked where to get nirs2img script. Here it is. The download link is at the bottom of this article.

nirs2img is to create an image file from the input data. Then the
image file can be viewed by any fmri image viewing programs such as
xjview. This function requires function mni2cor and spm

function nirs2img(imgFileName, mni, value, doInterp, doXjview, bilateral)

imgFileName: the file name to be saved, e.g. ‘testnirs.img’
mni: Nx3 matrix, each row a coordinate in mni space
value: Nx1 matrix, each row is the value corresponding to mni
doInterp: 1 or 0 , whether or not do linear interpolation to
smooth data.
doXjview: 1 or 0, whether or not to view the generated image by xjview
now
bilateral: 1 or 0, whether or not the input mni is bilateral or not. If
bilateral, the first half points are considered as left side. There is no
interpolation between left and right side. (This argument is
useless if doInterp is 0)

output:
an image file whose name is specified by input

If you have mni points of probes (instead of channels), you may need to
convert first. Use function probe2channel

This function will write to a image file which can be viewed by xjview.
In xjview, you need to check render view.

Example:
nirs2img(‘nirs_test.img’, mni, value, 1, 1, 0);

Xu Cui
2009/06/11
last update: 2009/07/06: have an option that left and right do not
interpolate

nirs2img.m
mni2cor.m

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One Reply to “nirs2img, create an image file from NIRS data”

  1. Hi Dr. Xu,
    I am getting the following error when trying to run nirs2img.

    Invalid MEX-file
    ‘/Users/emilydoherty/Documents/MATLAB1/spm8/@file_array/private/mat2file.mexmaci64’:
    dlopen(/Users/emilydoherty/Documents/MATLAB1/spm8/@file_array/private/mat2file.mexmaci64,
    0x0006): Library not loaded: @loader_path/libmex.dylib
    Referenced from:
    /Users/emilydoherty/Documents/MATLAB1/spm8/@file_array/private/mat2file.mexmaci64
    Reason: tried:
    ‘/Users/emilydoherty/Documents/MATLAB1/spm8/@file_array/private/libmex.dylib’ (no
    such file), ‘/usr/local/lib/libmex.dylib’ (no such file), ‘/usr/lib/libmex.dylib’
    (no such file)

    Error in file_array/subsasgn>subfun (line 132)
    mat2file(sobj,dat,va{:});

    Error in file_array/subsasgn (line 70)
    subfun(sobj,double(dat),args{:});

    Error in spm_write_plane (line 33)
    V.private.dat = subsasgn(V.private.dat,S,dat);

    Error in spm_write_vol (line 83)
    V = spm_write_plane(V,Y,’:’);

    Error in nirs2img (line 104)
    spm_write_vol(V,M);

    I would appreciate any advice you can give. Thank you.

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