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)


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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
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