Thanks you lot. It looks that it might be really a cause. However, I got in trouble with this reorientation. I open one of my images and I got the picture like in stage1.jpg Then, I hit the little bar and I get the picture like on stage2.jpg (when I do the same for normalized image, the crosshairs appears somewhere at the middle). I move the crossahair back to the middle and then click on reorient button while I select all the images I need to reorient. I see the procedure completed and the date of my hdr files is updated. However, when I click on small button again I still get crosshairs as in the stage1.jpg. What am I doing wrong?
BTW, is it possible to automate this reorientation procedure or I have to make it manually every time? Where did the problem occurred originally: in scanner or in DICOM to ANALYZE conversion?
Thank you again!
On Wed, Jul 30, 2008 at 4:36 PM, Darren Gitelman <[log in to unmask]>
My guess is that the origin of the images is not being set correctly in the small voxel images unless you normalize them. Try displaying an image and clicking the little bar above the image coordinates. This will display the image and crosshairs in relation to the actual origin. You may find that on the non-normalized images the crosshairs are not near AC-PC. If so you will need to re-orient the images so that the crosshairs are correct relative to AC-PC and then redo the stats.
I don't expect them to appear exactly at the right place. I am using functional localizer technique and I know in advance where more or less my region should appear. Specifically, fusiform gyrus can't appear in frontal lobe. The less preprocessing we do the better, so I prefer not to make normalization when I can localize my ROIs without it.
On Wed, Jul 30, 2008 at 3:36 PM, John Ashburner <[log in to unmask]>
If images are not spatially normalised, then there is no reason why the
activations should appear in the appropriate place on the glass brain. What
I can't figure out is why you appeared to get the activations in the right
place when using your normal resolution data.
On Wednesday 30 July 2008 12:00, Vadim Axel wrote:
> I am scanning with the following voxel resolution: 1.56 x 1.56 x 2.4
> Unless I do normalization (voxel size: 2x2x2) I am getting the activation
> totally misplaced in glass brain (see not_normalzied screenshot; the
> activations should be in temporal - occipital regions). Normalization
> solves the problem (see normalized screenshot). With normal resolution
> scanning (voxel 3.13 x 3.13 x 4) I get standard activations without
> normalizing data as well as with normalization.
> Any idea?