On 3 Sep 2018, at 10:41, Tabassi Mofrad, F. <[log in to unmask]> wrote:

Dear Matthew,

Yes, the ROI lines up perfectly on the standard image in the reg directory.

Kind regards,

Simin

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From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Matthew Webster [[log in to unmask]]
Sent: 31 August 2018 18:06
To: [log in to unmask]
Subject: Re: [FSL] Transforming an ROI mask in standard space into functional space

Hello,

 Can you confirm that your ROI lines up perfectly on the standard image in the reg directory?

Kind Regards

Matthew

--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

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

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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

  

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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 Regards

Matthew

--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 29 Aug 2018, at 17:28, Tabassi Mofrad, F. <[log in to unmask]LEIDENUNIV.NL> wrote:

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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