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Hi - yes, it sounds like you need registration/resampling, have a look at the ApplyXFM and Flirt GUIs and manual pages for these. Cheers. On 1 Jun 2007, at 01:12, Dianne Patterson wrote: > Dear Group, > Now I can see my binary images (thankyou) and I converted them from > analyze to nifti_gz with avwchfiletype. > The binary mask is 91x109x91 and the voxels are 2x2x2. > I want to display them in the space of my structural images (that > is, I want to overlay/add them to the structural images). The > structural image is 256x256x152 and 1.09375x1.09375x1.4. > I tried avwcpgeom struct.nii.gz frontal_lobe_R.nii.gz > but the resulting image was discombobulated (instead of a frontal > lobe mask, I had lines and spots of white spread all over the black > background. However, all of the dimensions were right (now > equivalent to the structural image. > > I tried avwcpgeom with the -d option and it correctly changed the > voxel size, left the image looking intact (looked like a frontal > lobe mask)...but I think I need to reslice the image...there is a > utility in spm reorient.m that I suspect will do the trick...but > I'm wondering if there is some way to successfully reslice the > image with the fsl utilities. > > OR Perhaps I should be doing something else...like registration? > Please let me know if i am on the wrong track completely. > > Thankyou so much, > > Dianne > > -- > Dianne Patterson, Ph.D. > [log in to unmask] > ERP Lab > University of Arizona > 621-3256 (Office) > > > On 5/31/07, Dianne Patterson <[log in to unmask]> wrote: > Wow...thankyou so much...that did the trick...I hadn't seen those > tiny little boxes. > > -Dianne > > > On 5/31/07, Peter Fried < [log in to unmask]> wrote:Hi Diane, > > It sounds like you might just need to change your window/leveling. > Are the > Min and Max values near the top of the screen (in fslview) at 0 and > 0? If > so change the Max value to 255 (the max value from avwstats++ -R). > > Hope this helps. > > -Pete > > > Dear Group, > > Any recommendations? > > Has anyone successfully used a set of rois (I am familiar with > the AAL > > library) to display in fslview as overlays? > > I gather I would need to reslice them to display them as a layer > on one of > > my anatomical images...but right now, I can't even view one by > itself (see > > below) > > ============================================================= > > I am also having trouble displaying the simple binary mask file > (img/hdr) > > in > > fslview. > > -I'm using a mask of the right frontal lobe...so it is nice and > big...not > > just lost in the image somewhere. > > All I see is black. > > -I used avwstats++ -r -R to get the min max voxel intensities and it > > reports > > 0 and 255. > > -I used avwstats++ -x to locate a max intensity voxel...but when > I went to > > that location I still only saw black, (although fslview reports > the voxel > > as > > having the value 255, it displays only the background black. > > -Shifting the transparency slider makes no difference. > > -If I display the image in ImageJ, I see the white mask of the > R_frontal > > lobe as well as the black background. > > -SPM5 also displays the image with no problem. > > -FSLview displays other *nii and * nii.gz files with no issue, > both the > > binary masks bet2 created and all of my other MR images. > > The little eye is checked on the lower right of fslview > indicating that > > the > > image should be viewable. toggling it makes no difference. > > -I presume the images are the old style img/hdr file...but I > thought nifti > > viewers, and especially fslview, could handle that... > > so I'm a little perplexed... > > > > Any thoughts on the source of my troubles would be greatly > appreciated. > > > > Thanks very much, > > > > -Dianne > > -- > > Dianne Patterson, Ph.D. > > [log in to unmask] > > ERP Lab > > University of Arizona > > 621-3256 (Office) > > > > > > -- > > Dianne Patterson, Ph.D. > [log in to unmask] > ERP Lab > University of Arizona > 621-3256 (Office) > > > > -- > Dianne Patterson, Ph.D. > [log in to unmask] > ERP Lab > University of Arizona > 621-3256 (Office) ------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---