Hi Brian (re-sent with email history). Thanks for your recommendation. I've tried your suggested solution but I only get the following error. I've tried looking through the details of the flirt command but I cannot understand why it's arising.
>flirt -in avg152T1_brain.nii.gz -ref task_deact.img -applyxfm -init difference_matrix.mat -out cropped_MNI
>terminate called after throwing an instance of 'NEWMAT::IncompatibleDimensionsException'
>Aborted
Would you have any advice here?
Thanks for all your help
***
Hi,
My guess is that SPM has cropped the image. the spm5 viewer I believe uses
the mm coordinates to render. FSLview requires identical number of voxel
dimensions. If you type fslinfo, you should notice the dimension
difference. You can use FLIRT to provide the appropriate crop.
You need to use fslhd to look at the qto_xyz matrices from the MNI
template and the cropped image.
e.g.
cropped image:
qto_xyz:1 -2.000000 0.000000 -0.000000 78.000000
qto_xyz:2 0.000000 2.000000 -0.000000 -112.000000
qto_xyz:3 0.000000 0.000000 2.000000 -50.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
mni template:
qto_xyz:1 -2.000000 0.000000 -0.000000 90.000000
qto_xyz:2 0.000000 2.000000 -0.000000 -126.000000
qto_xyz:3 0.000000 0.000000 2.000000 -72.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
Taking the difference between the centres gives a transform matrix of
1 0 -0 -12
0 1 -0 -14
0 0 1 -22
0 0 0 1
Then use:
flirt -in image_to_crop -ref cropped_image -applyxfm -init
difference_matrix.mat -out cropped_mni
In your case image to crop would be MNI152. difference_matrix.mat is what
is mentioned above.
The output image should now overlay.
cheers,
brian
> Hi, A basis question, but I am hoping to open results obtained using spm5,
> normalized to the MNI152 brain, in fslview. I can open both the spmT map
> and the MNI152 in the spm5 viewer, but when I open them in fslview it says
> the dimensions of the images differ. Can anyone explain why this is?
> Thank you very much in advance
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