Hi Watson and McLaren, thanks for your responses, it helps me understand more.
After the checking, I've found that the value read by spm_read_vols(SPM.xY.VY) is scaled, the scaled value is in pinfo.
1. I am curious why these voxel values should be scaled ?
2. How this scale be calculated ? Because I've tried many packages in R (nifti / fmri / AnalyzeFMRI) and voxel values read by these packages are unscaled. Is there any difference to analyze data with scaled and unscaled voxels ?
(values from spm_read_vols) = (values from R packages)*(scale number in pinfo)
I've tried to check spm_slice_vol.m, but it seems be complied in .mex file and I can't see the origin code.
Thanks for your help, sincerely
On Tue, 24 Dec 2013 13:14:35 -0600, MCLAREN, Donald <[log in to unmask]> wrote:
>There are likely two differences:
>(1) When you display things in SPM, the values are interpolated, turning
>the interpolation off should fix the issue if you told the program to
>display the same image that you loaded;
>(2) SPM.xY.VY.pinfo is likely different from hdr.pinfo, when its created
>from hdr=spm_vol(filename). The pinfo field contains scaling information.
>The pinfo field is modified during the 1st level model creation to make the
>mean 100. Thus, it will give you different values than the unscaled image.
>Hope this helps.
>Best Regards, Donald McLaren
>D.G. McLaren, Ph.D.
>Research Fellow, Department of Neurology, Massachusetts General Hospital and
>Harvard Medical School
>Postdoctoral Research Fellow, GRECC, Bedford VA
>Office: (773) 406-2464
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>On Tue, Dec 24, 2013 at 12:21 PM, Chris Watson <
>[log in to unmask]> wrote:
>> How are they different?
>> On 12/24/2013 09:40 AM, Philip Lin wrote:
>> Hi all,
>> I have a question about voxel values in SPM. If I read an image into SPM8 and use GUI (Display) to show the target image, the value for each voxel means intensity. If I read the same image by using spm_read_vols(SPM.xY.VY), the values for each voxel is apparently different to intensity. What's the difference between them ? What's the meaning of values from spm_read_vols ?
>> Thanks if there's any help, sincerely
>> Philip Lin