My analyze files were produced through MRIcro. Since my last mail I have
looked at phantom images with markers for left and right. I have set the
default LR flip in MRIcro to ‘1: RPI --> LAS = SPM2’ and the
defaults.analyze.flip value in SPM2 to 1. When I preview my phantom
image in MRIcro, the image satisfies that if ‘defaults.analyze.flip=1’
in ‘spm_defaults.m’ then left on right, right on left.
If I then display this image in SPM2 the image returns to its left on
left, right on right orientation with a negative x coordinate. Am I to
understand therefore that this negative x coordinate is just indicative of
a flip having taken place so that my image displays on the screen in the
same orientation as the template images (e.g. EPI.mcn). If so, will this
flip automatically be applied during the normalization process due to the
default.analyze.flip being 1?
With many thanks in advance
Jenny
On Thu, 20 Jan 2005 12:15:24 +0000, John Ashburner
<[log in to unmask]> wrote:
>When images are displayed in SPM, there is usually a negative voxel size
>shown. The voxels of proper Analyze images should be stored so that x
>increases from right to left, y increases from back to front, and z
increases
>from bottom to top. The T&T system has the x going from left to right.
>Therefore a flip is needed to map from the way the data are stored, to
the
>way that they are displayed. In order to do this, SPM needs to consider
that
>one of the voxel sizes is reversed. For reasons that are more to do with
>psychology than maths or physics, I chose to show the left-right
direction as
>reversed.
>
>Whether the co-ordinates should be flipped really depends on how the
Analyze
>images were created. Some labs store their voxels with x increasing from
>left to right, in which case a flip would be the wrong thing to do. Labs
>with their data stored in this order should have their defaults changed
>(permenantly) in order to tell SPM the order of the voxels, and whether
>flipping is necessary.
>
>I'm not sure how you got your data into Analyze format, so can't comment
on
>the order that the voxels are stored and whether flipping should be done.
>
>There is a little more info about this at
>http://www.fil.ion.ucl.ac.uk/spm/software/spm2/#Compatability
>and also on pages 10 and 11 of
>http://www.fil.ion.ucl.ac.uk/spm/doc/books/hbf2/pdfs/Ch2.pdf
>
>
>Best regards,
>-John
>
>> I was hoping that you might be able to give me some assistance on a
>> technical problem I am currently having during the spatial pre-
processing
>> of fMRI data using SPM2.
>>
>> I have 2 data sets. The first of which (data set 1) appears to be being
>> processed as expected. The dimensions of the 3mm anatomical slice used
for
>> co-registration and for determining parameters for normalisation are
>> 64x64x64 (with a voxel size of 3x3x3). The dimensions of the fMRI data
set
>> are 64x30x64 (with a voxel size of 3x6x3). This produces a final
>> realigned, normalised, smoothed image with a voxel size of -2x2x2.
>>
>> Images from the second data set (data set 2) however, are being
initially
>> displayed with dimensions of 64x64x64 (with a voxel size of -3x3x3) for
the
>> 3mm anatomical data and dimensions of 64x30x64 (with a voxel size of -
>> 3x6x3) for the fMRI data set. The final realigned, normalised, smoothed
>> images have a voxel size of -2x2x2.
>>
>> However as you can see from the images attached, the final images
produced
>> from data set 2 are smaller in comparison to those produced from data
set
>> 1, even though the voxel size apparently has remained the same.
>>
>> Initially, with data set 2, I changed the ‘resize {x}’ value to -1 to
flip
>> all of the original images to cancel the negative voxel size. However,
>> this didn’t make any difference to the final realigned, normalised,
>> smoothed images, which still have a voxel size of -2x2x2 and were still
>> smaller on the ‘display’ than those from data set 1.
>>
>> As I am new to using SPM2, I cannot think of what the problem might be
and
>> why the final images are being produced with a negative voxel size,
which
>> seems to be independent of whether the original images (those before
pre-
>> processing) have a negative voxel value or not and why the images
appear to
>> be smaller on display.
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