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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 >