Reading bhx files:
Hello Dr. Jack,
Sorry for the delayed response. Please see the information below from the
textbook's author:
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We downloaded the MRIcroN source code, downloaded the compiler he uses,
compiled MRIcroN, ran it through a debugger, and finally figured out what we
think is wrong. The original .bxh files don't have any sort of voxel
spacing so the voxel spacing gets set in the Analyze headers to 0. MRIcroN
actually uses this data to calculate a fake orientation matrix, and so
depends on those fields being filled in. Presumably the SPM error that the
original submitter mentioned is related to this too (though we have not been
able to reproduce this).
We suggest the following strategy. In the BXH file, replace:
<dimension type="x">
<size>64</size>
</dimension>
<dimension type="y">
<size>64</size>
</dimension>
<dimension type="z">
<size>14</size>
</dimension>
<dimension type="t">
<size>50</size>
</dimension>
with:
<dimension type="x">
<size>64</size>
<spacing>3.75</spacing>
<direction>-1 0 0</direction>
</dimension>
<dimension type="y">
<size>64</size>
<spacing>3.75</spacing>
<direction>0 -1 0</direction>
</dimension>
<dimension type="z">
<size>28</size>
<spacing>5</spacing>
<direction>0 0 -1</direction>
</dimension>
<dimension type="t">
<size>50</size>
<spacing>2000</spacing>
</dimension>
This should allow the resulting Analyze files to be readable in MRIcroN.
The direction vectors are only of use if generating NIFTI, and in that case,
we would need to provide another executable and perhaps update the tutorial
text, but that would allow orientation labels to be reported accurately in
most viewers. Note also that the cropping is intentional. These images have
an artifact in them that is visible on the raw data; the goal of the
associated exercises was to understand this artifact.
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