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Hi Michael,

Nudge (Nudge_gui on the mac) is an FSL tool that allows you to translate, rotate and scale a mask manually and generate a new transform matrix for it...normally this is used to improve registration...but I think it would allow you to do what you want as well...you'll find it mentioned here and there in the FSL archives.

My biggest hurdle with ImageJ was making sure my image got properly flipped around to view the way that I wanted to in ImageJ and then got back into the right format for fsl...

ImageJ won't read nii.gz files but if you gunzip the files, it'll read nii files (with the nfti plugin available on their plugins page...).  There is also an analyze plugin, if that is what you need.

ImageJ allows you to create rois and save them independently of the images themselves...and, like fsl, there is a helpful community of people who will share suggestions and send you tools...

I hope that is useful,

-Dianne


On Wed, May 28, 2008 at 2:05 PM, Lipton, Michael <[log in to unmask]> wrote:
Hi Diane,

We did of course apply a single ROI to each coregistered subject image. However, I am now dealing with a reviewer who wants to know results based on "untouched" subject data...

Is there anything I should know about doing this in ImageJ? What is "nudge" that you refer to?

Thanks,

Michael


-----Original Message-----
From: FSL - FMRIB's Software Library on behalf of Dianne Patterson
Sent: Wed 5/28/2008 1:59 PM
To: [log in to unmask]
Subject: Re: [FSL] ROIs

I'm using ImageJ to do something like this....though now that I think about
it...couldn't you create rois on a standard (or one subject) and then
register them to the new subject and use nudge to move them into position?

I'd love to see a more elegant solution, though.

-Dianne

On Tue, May 27, 2008 at 6:29 PM, Michael Lipton <[log in to unmask]>
wrote:

> Hi,
>
> I am looking to do an ROI analysis where I would like to place multiple
> regions of exactly the same size and shape on images from multiple patients.
> This would require copying and pasting ROIs and moving them into position.
> Can ROIs be duplicated and moved in FSL View?
>
> Thanks,
>
> Michael
>
>


--
Dianne Patterson, Ph.D.
[log in to unmask]
ERP Lab
University of Arizona
621-3256 (Office)




--
Dianne Patterson, Ph.D.
[log in to unmask]
ERP Lab
University of Arizona
621-3256 (Office)