>I would stop there - I don't think there's any point going further unless you can be sure what space this ROI relates to?
>
>Cheers, Steve.
Going through this process will allow me to test that. I know pretty much where the ROI is supposed to be, so once I have ROI and structural image in with the same dimensions, I can look at it and verify whether it puts the ROI in the right spot. If so, great. If not, I've wasted some time, but I can live with that. I'm low on options right now -- I've spent months trying to get answers from the source of this data.
Thanks,
-Ben
On Tue, 29 Jul 2014 08:09:17 +0100, Stephen Smith <[log in to unmask]> wrote:
>Hi
>
>On 28 Jul 2014, at 21:17, Benjamin Philip <[log in to unmask]> wrote:
>
>> I am in the unfortunate position of having received a ROI in 3x3x3mm space, which is not the space of my data - I'd like to get this ROI into 2x2x2 standard space, once it's there I know what to do with it.
>>
>> Added complication: I don't have ANY 3x3x3 brains on hand. To make our lives easier for my first attempt, let's assume that the space we're looking for is just a downsampled version of the MNI standard brain. (If it's not, I will need to get my hands on the source data, but if that were easily done I wouldn't be here.)
>
>I would stop there - I don't think there's any point going further unless you can be sure what space this ROI relates to?
>
>Cheers, Steve.
>
>
>>
>> How do I go about converting the ROI into 2x2x2 space? Obviously, I need to preserve its location as best as possible. I tried to start out by downsampling a standard brain via:
>>
>> flirt -interp nearestneighbour -in bg_image -ref bg_image -applyisoxfm 3 -out 3bg_image -omat 3mm_to_2mm.mat.
>>
>> My hope was I could then put that transformation matrix into:
>>
>> flirt -in <3mm ROI> -out <2mm ROI> -ref <standard brain> -applyxfm -init 3mm_to_2mm.mat.
>>
>> Unfortunately, my first flirt command changes around the spatial dimensions, not just the voxel counts. It goes down to 2x2x2 but the space goes from 91x109x91 (standard bg_image) to 60x72x60, while my ROI is 48x64x48. So, I'm clearly missing something here.
>>
>> Anyone know how to accomplish this?
>>
>> Thanks!
>>
>> -----
>> Benjamin Philip, Ph.D.
>> Postdoctoral Fellow - Freylab
>> University of Missouri
>> 206 Melvin H. Marx Bldg
>> 1416 Carrie Francke Drive
>> Columbia, MO 65211
>> [log in to unmask]
>
>
>---------------------------------------------------------------------------
>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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