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Subject:

Re: Transforming an ROI mask in standard space into functional space

From:

"Tabassi Mofrad, F." <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Fri, 7 Sep 2018 13:42:56 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (224 lines)

Dear Matthew,

You are right. Thank you, that was helpful.

Kind regards,
Simin

________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Matthew Webster [[log in to unmask]]
Sent: 06 September 2018 13:56
To: [log in to unmask]
Subject: Re: [FSL] Transforming an ROI mask in standard space into functional space

Hello,
         Iíve looked at your file and it is pretty much identical to the images I generated ( and in a similar location ) - how are you finding it to be outside of the brain? For the inverse, you simply need to use invwarp on the example_func2standard_warp.nii.gz file and pass that to applywarp.

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

> On 5 Sep 2018, at 17:31, Tabassi Mofrad, F. <[log in to unmask]> wrote:
>
> Dear Matthew,
>
> If I understand it correctly, to do the transformation an inverse of example_func2struct, calculated via:
>
> convert_xfm -omat highres2example_func.mat -inverse example_func2highres.mat,
>
> as well as the inverse of the non-linear transform highres2standard_warp are needed to feed the command
>
> applywarp -i <file name> -r reg/example_func.nii.gz -o <filename_func> --postmat=reg/highres2example_func.mat -w reg/highres2standard_warp_inv
>
> Please, could you let me know in what stage you have used an inverted example_func2standard_warp? Maybe I have missed one stage? I have also uploaded thetransformed ROI.
>
> Kind regards,
> Simin
>
>
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Matthew Webster [[log in to unmask]]
> Sent: 05 September 2018 14:59
> To: [log in to unmask]
> Subject: Re: [FSL] Transforming an ROI mask in standard space into functional space
>
> Dear Simin,
>    Thank you for your upload, Iíve tried the commands you listed ( as well as using an inverted example_func2standard_warp for the transformation ) and the mask lines up with the brain in all cases ( example screenshot below for standard,highres and example_func ). Can you recheck your warped ROIs ( and uploaded them if they donít match the images below )?
>
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital<mask.png>
> University of Oxford
>
>> 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 ópostmat 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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