Dear Naama,
sorry I have not followed all the emails about this
transformation problem but it seems that everything is
coming from the misregistration of your "best" target
onto the MNI152. Have you identified this former and
try to see if you can obtain something better just
playing with Flirt and this target?
Most of the time, Flirt happens to be much more robust
than areg, the affine registration used to transform
the best target into the MNI space in the TBSS
protocol.
Hope this helps,
Gwenaelle
--- Naama Barnea-Goraly <[log in to unmask]> a écrit
:
>
> Dear Christian and FSL experts,
>
> avwsize gives the same dimension for the mean_FA and
> the MNI
> template. Anything else I can look for?
>
>
> $ avwsize mean_FA
> dim1 182
> dim2 218
> dim3 182
> dim4 1
> pixdim1 1.0000000000
> pixdim2 1.0000000000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
>
> $ avwsize MNI152.nii.gz
> dim1 182
> dim2 218
> dim3 182
> dim4 1
> pixdim1 1.0000000000
> pixdim2 1.0000000000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
>
> Thanks,
>
> Naama
>
>
>
>
> >>
>
>
>
> >>> Hi,
> >>>
> >>> Your voxel dimensions in Z seem to be wrong.
> Check with avwsize
> >>> filename that the voxel size in Z (pixdim3) is
> what it should be.
> >>> If not, you can use avwedithd to change this.
> >>> cheers
> >>> christian
> >>
> >>
> >>
> >>
> >>>>
> >>>>
> >>>> After some off-list clarifications (sorry, and
> thanks,
> >>>> Andreas!). I would like to explain that the
> image I previously
> >>>> sent was an artificial image created by me, not
> my mean_FA
> >>>> image. It was a superimposed image of the
> mean_FA and and MNI
> >>>> template, I made the template lighter so that
> the differences
> >>>> would be apparent, it is not an intensity drop.
> >>>>
> >>>> To make things clearer I am attaching an image
> of my mean_FA and
> >>>> (just for reference) the MNI template.
> Obviously they are not
> >>>> registered.
> >>>> I would appreciate any advice on why this
> happened.
> >>>>
> >>>> Thanks much!
> >>>>
> >>>> Naama
> >>>>
>
> Naama Barnea-Goraly M.D.
> Research Associate
> Center for Interdisciplinary Brain Sciences Research
> Stanford University Division of Child and Adolescent
> Psychiatry
> 401 Quarry Rd. MC 5795
> Stanford University School of Medicine
> Stanford, CA 94305-5795
> fax: (650) 724-4794
> Phone: (650) 724-3779
>
>
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