Hi - sorry, these dimensions are in voxels not mm - so if you're
estimating the ROI from FSLView you need the leftmost co-ordinates
(voxels) not the mm co-ords. The voxel co-ordinate frame starts at
[0,0,0] in the corner of the image and never goes negative.
Cheers.
On 15 Oct 2007, at 04:01, Catherine Warrier wrote:
> Dear list,
>
> I am brand new to FSL and am having trouble using the fslmaths -roi
> function. I have a number of
> volumes with two regions of interest each, one on the right and one
> on the left. I need to extract
> data from the left and right separately and would like to avoid
> manually erasing each one
> separately. I understand that this function sets everything
> outside the designated region to 0, so
> I want to select one hemisphere at a time. I thought I understood
> this but I can only seem to
> generate empty volumes.
>
> Here's the syntax:
> fslmaths input -roi <xmin> <xsize> <ymin> <ysize> <zmin> <zsize>
> <tmin> <tsize> output
>
> Here's an example of what I've tried:
> fslmaths input -roi -75 75 -40 160 -40 130 0 1 output
>
> specifying the left hemisphere and the entire y and z dimensions.
> I only have one volume, so tried
> timepoint 0 with 1 timepoint as well as 1 and 1. I also tried
> decreasing the extent of the y and z
> dimensions. Tried playing with the min and max of the viewer when
> viewing the resulting volume,
> but it is truly empty. Tried the function with and without
> extensions on the input/output files...
>
> What am I doing wrong? Any suggestions would be greatly appreciated.
>
> Thank you,
> Catherine
>
>
> ~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-
> Catherine Warrier, PhD
> Research Assistant Professor, Knowles Fellow
> Auditory Neuroscience Laboratory
> Northwestern University
> ~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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