OK I think I found the parameter for scaling: they are hdr.dime.scl_slope and hdr.dime.scl_inter. Now I know how these packages works, and I can scale the voxel intensity myself if I want. Sorry for the cursory questions, and thanks for the good tool! -Wei
When reading a nifti file I found the voxel gray values are different with other tools. What I did is:
- 'untouch load' the file: fmri_mean = load_untouch_nii(.../meanfM00223_004');
- print voxel value of mri_mean.img(32,32,23). The value is 9506.
- But when I open the same file with fslview, I found the same voxel has different value. And other voxels are also different. the fslview snapshot is attached. Because in fslview the voxel coordinates begins from 0 to dim-1, the same voxel in fslview has coordinate [31 31 22].
- Use the application 'Imageviewer' from itk, and found the voxel value is same with fslview. Also attached snapshot. Same to fslview the coordinate are [31 31 22] for the same voxel.
- check the header of the nifti file by fsl tool 'fslhd':
datatype 4
nbyper 2
bitpix 16
That means it's int16.
-Check the fmri_mean structure in matlab, and found the data type is 4:
datatype: 4
bitpix: 16
But why did your nifti tool give different gray value with other packages? I put all the snapshot and the nifti files at www.sci.utah.edu/~weiliu/q01/ for your reference.
I've downloaded and did the configuration in .emacs file. But when I open a .m file with emacs, it gave error "can not find mlint file". My Matlab is not installed on the local file system, but on a network directory. I'm using opensuse 10.3. Any one having experience on this can give me a clue? I guess I have to edit the matlab.el file to tell the add-on where the matlab bin directory is. Thanks.
