I don't quite know what atlas you used to generate your ROI but it is not a size that I recognise.
Regardless of this, you can resize it by using the coordinate information.
The commands you use for this are:
flirt -in yourROI -ref MNIspaceImage -usesqform -out newROI
fslmaths newROI -thr 0.5 -bin newROI
This will give you a new binary ROI that has a size that matches the dimensions you need and also shifts it into the correct location. The latter part (shifting it to the right position) is also crucial, not just changing the size.
All the best,
> On 1 Aug 2017, at 19:39, Isha Dhingra <[log in to unmask]> wrote:
> Hi Mark,
> Thanks for your message and sorry about the earlier sketchy question! So what we're trying to do is calculate activated voxels in our contrast images using a ROI mask. Our contrasts and ROI mask are both in MNI space. We have done the registration and normalization steps, binarized all our contrasts and removed any NaNs. Now we want to multiply our binarized nonan contrasts X the ROI mask and then calculate the number of activated voxels. However, when we perform the multiplication using fslmaths -mul, we get this error:
> 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
> libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException
> Abort trap: 6
> We have ensured that both our ROI mask and contrast image have FLOAT data structure (initially one was FLOAT and the other INT16). Currently the only differences between the two are the dim parameters in the header that I mentioned in my earlier message. If we use fslcpgeom and change these parameters, the falmaths -mul works fine with no errors, which is why I believe this is the way forward. However, the output is no good because as I learned from an earlier thread, fslcpgeom alters only the header and not the actual image. Therefore, we need to figure out how to change the actual dimensions of the ROI mask to make it multiply-able by our contrasts, i.e. the same size.
> We created our ROI using FSLview and an atlas, and everything (ROI mask, all contrasts) has been registered to MNI space.
> Thanks again,