Dear Pasi,
> McFLIRT still doesn't work. Funny thing is, that
> exactly the same data goes through for example Susan or Melodic with no
> problems. Mcflirt gives segmentation violation, whatever I try. If the
I have had a look at your data and discovered the problem.
You have only 2 slices, and mcflirt requires at least 3 slices and a
24mm FOV in z, in order to be able to calculate 3D neighbourhoods.
At present we do not have a 2D mcflirt option.
However, this problem can be easily overcome by padding out your data
with the existing slices. That is, making a new volume that is
128x128x6x60 simply by copying each slice 3 times. To do this, use the
following avwroi and avwmerge commands:
avwroi data d0 0 128 0 128 0 1 0 60
avwroi data d1 0 128 0 128 1 1 0 60
avwmerge -z thickdata d0 d0 d0 d1 d1 d1
this saves the individual slices as d0 and d1, then concatenates them in
z to create the new volume, thickdata.
In order to assure the FOV is large enough, I also suggest modifying the
original voxel size in "data" (before you do the above) so that the z
thickness is 8mm.
Once you've done this you can happily run mcflirt on "thickdata".
The output will also have 6 slices, which can then be reduced to the
original 2 slices by again using avwroi like this:
avwroi thickdata_mcf data_mcf 0 128 0 128 2 2 0 60
This then creates the file "data_mcf" containing the motion corrected
time-series with the original sizes of 128x128x2x60.
Hopefully this will sort out all of your problems.
Best wishes,
Mark
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