Hi Alle Meije,
> The 'mean functional' and 'mean structural' mask files that show aligned in
> FSLeyes have dimensions of 60x72x60 and 53x63x52 voxels, respectively and
> the same voxel sizes in mm.
The problem is possibly due to the fact that the images have different
fields-of-view. You could try adding some padding to the smaller image
(the structural?), and then re-running flirt. You can add padding
using fslroi, by entering negative values for the min parameters, and
extra-large values for the size parameters.
Cheers,
Paul
On 22/10/2018, Alle Meije Wink <[log in to unmask]> wrote:
> Dear spatial experts,
>
> In an external data set of structural and functional MR imaging data, both
> are in MNI space but with different voxel resolutions and a different
> bounding box. If I open a functional and structural image together in
> FSLeyes, they are aligned.
>
> To make a grey matter mask for the functional images, I resampled the group
> GM density maps at the same voxel resolution (3 mm) as the functional data,
> with flirt:
> flirt -in gmgroup -ref $FSLDIR/data/standard/MNI152_T1_1mm_brain -out
> test -applyisoxfm 3
> In FSLeyes everything still looked OK.
>
> But to apply the mean GM mask to a functional scan, even when it has the
> same voxel size, it needs to be resampled in the same bounding box,
> otherwise fslmaths will give
>
> WARNING:: Inconsistent orientations for individual images in pipeline!
> Will use voxel-based orientation which is probably incorrect -
> *PLEASE CHECK*!
>
> Image Exception : #3 :: Attempted to multiply images/ROIs of different
> sizes
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> Aborted
>
> So I tried both
> flirt -in gmgroup -ref sub-001/func/bold -out gmgroup_3mm -applyisoxfm 3
> and
> flirt -in gmgroup -ref sub-001/func/bold -out gmgroup_3mm -applyxfm
> but both of the versions of the output, when shown in FSLeyes together with
> a functional image, show a shift between the functional and structural
> images.
>
> The 'mean functional' and 'mean structural' mask files that show aligned in
> FSLeyes have dimensions of 60x72x60 and 53x63x52 voxels, respectively and
> the same voxel sizes in mm.
>
> The culprit seems to be the s-form (or q if you like) which has centre of
> gravity [90.000 -126.000 -72.000] for the structural scans and [78.000
> -112.000 -70.000] for the functional scans.
>
> Is there a way to resample one into the other's space, (i.e. both 60x72x60
> voxels or both 53x63x52) while still being aligned?
> Obviously I would like to stay away from performing coregistrations on
> already aligned and registered data!
>
> Many thanks
> Alle Meije
>
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