Hi Dianne,
I am not sure, but you might want to have a look at the script
flirt_qsinit.sh that distributed on the list earlier. I used that with
applyXFM and flirt to prepare my VOI's for FSL.
Regards,
Benny
> 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
> ------------------------------------------------------------------------
> ---
>
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