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On 31 Aug 2018, at 09:54, Tabassi Mofrad, F. <[log in to unmask]> wrote:
Dear Paul,
Yes they overlap. Maybe I should mention that in preprocessing I did a nonlinear registration. Would that be a problem?
Best,Simin
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of paul mccarthy [[log in to unmask]]
Sent: 30 August 2018 12:01
To: [log in to unmask]
Subject: Re: [FSL] Transforming an ROI mask in standard space into functional space
Hi Simin,
Could you double check that your highres -> standard registration was successful? Open both highres2standard.nii.gz and standard.nii.gz in FSLeyes/FSLView and check that they overlap.
Cheers,
Paul
On 30 August 2018 at 10:54, Tabassi Mofrad, F. <[log in to unmask]> wrote:
Dear Matthew,
I transformed the ROI to highres space. The RIO is inside the brain however, not correctly where it should be. To invert the warp I have used:
invwarp --ref=highres --warp=highres2standard_warp --out= highres2standard_warp_inv
Kind regards,Simin
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Matthew Webster [[log in to unmask]]
Sent: 29 August 2018 18:37
To: [log in to unmask]
Subject: Re: [FSL] Transforming an ROI mask in standard space into functional space
Hello,To check your inverted warp is working can you try transforming the ROI to highres space ( e.g. -r reg/highres.nii.gz and drop the —postmat option ) and see if the ROI is aligned correctly with the highres image?
Kind RegardsMatthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
Dear FSL experts,
In order to transform an ROI mask in standard space into functional space I have used:
applywarp -i <file name> -r reg/example_func.nii.gz -o <filename_func> --postmat=reg/highres2example_func.mat -w reg/highres2standard_warp_inv
However, the mask falls outside of brain after transforming it into functional space.
Please could you let me know what the reason is?
Thanks & kind regards,Simin
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