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Hi Paul

I used the following commands to create the mask in a PreCentral Region:

fslmaths avg152T1_brain.nii.gz -mul 0 -add 1 -roi 61 1 51 1 65 1 0 1 PreCentPoint -odt float

fslmaths PreCentPoint -kernel sphere 5 -fmean PreCentSphere -odt float

 

I have tried other ‘standard images’ to start with but makes no difference.

The mask created also displays properly as an overlay on any standard space image.

 

I’m running in the featquery gui. I do not get an error as such. The html just shows the mask region as being way outside the brain and thus the statistics published are all zeros.

 

Thanks for the help.

 

David

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of paul mccarthy
Sent: 23 February 2015 09:01
To: [log in to unmask]
Subject: Re: [FSL] featquery

 

Hi David,

 

Could you please tell me how you created the mask, and give an example of one of the featquery commands that failed?

 

Cheers,

 

Paul

 

 

On Fri, Feb 20, 2015 at 4:58 PM, Dr. David Watson <[log in to unmask]> wrote:

Dear Mailbase
I have recently been trying to use featquery to interrogate some FEAT results using a mask. I created the mask in standard space (to use with all FEAT directories) but when I try to apply it things appear to go wrong. In the html files the mask is displayed completely outside the brain of all subjects with changed coords as through the mask as been rewarped in space. I understood from the documentation that featquery would automatically identify the mask space and transform it appropriately to each example_func space. The various mat files necessary are present in the reg directories and all FEAT directories also have a sub-directory called reg_standard which contains the cope images transformed into standard space. Has anyone any suggestions as to what I'm doing wrong. Thanks in advance.

Dr. David Watson
Research Fellow
CISC
University of Sussex
Falmer
UK

 


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