On Tue, May 19, 2009 at 2:24 PM, Xiang Wu <[log in to unmask]> wrote:
> Thanks a lot, I checked the usages of spm_vol and spm_read_vols. I figure
> your sample script could be simplify further as below:
>
> Say the roi file is roi.hdr (img, or in nii format) and con* image is
> con_0001.hdr (img).
>
> step 1: read the imformation of the roi and the con image
> V_roi = spm_read(roi.hdr);
> V_con = spm_read(con_0001.hdr);
This should be spm_vol('.img file')
>
>
> step 2: get the values stored in the roi and the con image
> (note, if use marsbar to define roi, export the roi mat file to images, and
> remember to use the con file as space during the exportation, so that
> xyz_roi=xyz_con)
> [Y_roi, xyz_roi] = spm_read_vols(V_roi);
> [Y_con, xyz_con] = spm_read_vols(V_con);
you dont need xyz, just Y = spm_read_vols(V);
>
>
> step 3: find the non-zero pixels in roi image, and extract these pixels
> values in con image
> pixel_non_zero_in_roi = find(Y_roi~=0);
> what_we_want = Y_con(pixel_non_zero_in_roi);
find already returns non zero indices, so just do - what_we_want =
Y_con(find(Y_roi));
>
>
> In addition, from the help file it seems the mask (roi file here) can be
> input into spm_read_vol, but I failed because I can't find the the format
> of
> that. Otherwise step 2 and step 3 can be combined and simplified further.
>
> Thanks Chris again.
> xiang
>
--
Research Associate
Gazzaley Lab
Department of Neurology
University of California, San Francisco
