just as an update, i tried using read_hdr, manually changing the offset in
matlab and write_hdr_raw to change it, but when i looked at the image in
display, it was all white and didn't work. so i used a workaround that i
believe is valid (someone please speak up if they think otherwise), namely i
segmented the single subject T1 in the canonicals directory, and used that
as a "transform" for the ROI's into template space. it looks like it worked
very well to me.


On Wed, Jul 29, 2009 at 12:07 PM, Dani Simmonds <[log in to unmask]>wrote:

> hi,
> i am using a program called medinria for dti fiber tracking, and using spm
> to normalize the data into mni space prior to running analyses. i also used
> wfu_pickatlas to define my ROIs for the analyses. i segmented the initial
> dti image to obtain transformation parameters and normalized it into the
> template space (using the default normalization parameters). i also used a
> script found here (
> to reslice the pickatlas ROIs into the same bounding box as the normalized
> dti image. however, when i loaded the images in medinria, i found that in
> the 2d views, they lined up perfectly, but in the 3d views, the ROI was
> quite a distance outside of the brain. as i investigated further (using
> spm_read_hdr), i noticed that the offset for the normalized dti images was
> 352, and for the ROIs was 0. that was the only difference i could find, and
> i assume that is what is causing my problem. how can i change this value in
> the hdr file, and should i change the dti image, or the ROI? thanks.
> dani