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On 4 Sep 2018, at 13:50, Tabassi Mofrad, F. <[log in to unmask]> wrote:
Dear Matthew,
Thank you. I have uploaded a zip file in the name of Mask.
Kind regards,
Simin
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Matthew Webster [[log in to unmask]]
Sent: 03 September 2018 13:57
To: [log in to unmask]
Subject: Re: [FSL] Transforming an ROI mask in standard space into functional space
Dear Simin,
Can you tar all the files involved ( example_func,highres,standard, warps, mats and ROI ) and upload to:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF
And we will look at what is happening?
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
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
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
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 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]> 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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