It should not make so much difference. The re-orientation pre-multiplies all
the matrices in the headers by the matrix generated from the parameters, such
that the relative orientations of the images (to each other) are conserved.
Best regards,
-John
On Thursday 31 July 2008 08:55, Vadim Axel wrote:
> Thank you Darrel. I very appreciate your help.
>
> My last question:
> As far as I understand the correct way is to make the same reorient to all
> the sessions of specific subject. However, do I have to make it after
> realign preprocessing stage (to all my sessions) or before.
>
> Vadim
>
> On Wed, Jul 30, 2008 at 8:08 PM, Darren Gitelman
<[log in to unmask]>wrote:
> > Vadim
> >
> > you have to enter the transformation coordinates in the boxes under the
> > images
> > Here are the steps
> > 1) Display the image to move and click the origin bar (the small thin bar
> > above the coordinates)
> > 2) The mm values should be [0 0 0]
> > 3) Click on the image until the crosshairs are where you want them
> > 4) The values in mm are the amount you have to move the images. Let's say
> > the values are [5 20 -10]
> > 5) Enter the negative of the values (i.e., [0 0 0] - [5 20 -10] = [-5 -20
> > 10]) in the right, forward and up boxes respectively.
> > 6) Click the reorient button and select the image(s) you want to
> > reorient. Voila they are reoriented.
> > 7) Check the image in display.
> >
> > Notes:
> > 1) Instead of clicking the image you can just enter values in the
> > reorientation edit boxes and watch where the crosshairs will move. This
> > is also what you will have to do to counter any rotations. (note the
> > rotations are in radians so usually very little movement is needed).
> > 2) You can semi-automate this by using the Util->Reorient function in
> > batch although you will need the proper 4x4 transformation matrix.
> > 3) You can select as many images that you want to move.
> >
> > This probably occurred because the voxel size is 1/2 and so the images
> > are shifted by that amount relative to the larger voxel sizes.
> >
> > Darren
> >
> > On Wed, Jul 30, 2008 at 10:50 AM, Vadim Axel <[log in to unmask]> wrote:
> >> Hi Darren,
> >>
> >> 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!
> >> Vadim
> >>
> >> On Wed, Jul 30, 2008 at 4:36 PM, Darren Gitelman
<[log in to unmask]>wrote:
> >>> Vadim
> >>> 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.
> >>>
> >>> Darren
> >>>
> >>> On 7/30/08, Vadim Axel <[log in to unmask]> wrote:
> >>>> 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]
> >>>>
> >>>> > wrote:
> >>>>>
> >>>>> 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.
> >>>>>
> >>>>> Best regards,
> >>>>> -John
> >>>>>
> >>>>> On Wednesday 30 July 2008 12:00, Vadim Axel wrote:
> >>>>> > Hi,
> >>>>> >
> >>>>> > 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?
> >>>>> >
> >>>>> > Thanks,
> >>>>> > Vadim
> >
> > --
> > Darren
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