On Thu, 3 Dec 2009 00:36:39 +0000, Kathy Pearson
<[log in to unmask]> wrote:
>Dear List,
>
>I am trying to determine if SPM8 will give the same output for 3D and 4D
>input. I start with the example of a simple realignment.
>
>First, using local data, I convert DICOM files to Nifti with dcm2nii. After
>generating both 3D and 4D *.nii, I compare these, reading with
>spm_vol/spm_read_vols, and see that the input volumes are considered
>identical. Realign, run with the defaults (separately for 3D and 4D),
>creates r* 3D and r* 4D volumes that are not the same. In x-y-z locations
>where the r* 3D and 4D volumes are unequal, the differences are all either
>plus or minus 1. For this data set, 1 happens to be the scl_slope value in
>the original Nifti input headers created by dcm2nii. Is it expected that
>the 3D and 4D realigned images would be different if the inputs are
>considered identical by SPM?
>
>Alternatively, using the SPM data set from MoAEpilot.tgz, I tried various
>methods to generate a 4D file that SPM reads to report identical values to
>those in the 3D Analyze input. The SPM "3D to 4D" utility output does not
>match although both input and output are INT16 -- absolute differences go
up
>to 0.05. The funused1 values in the 3D Analyze headers = 0.125. In the
>end, I set v.fname to '4D.nii' and v.n to [i 1] as I read the 3D volumes,
>thus writing a 4D.nii file with spm_write_vol that SPM reads back as
>identical to the 3D Analyze. Is there a better method to create a data set
>with 4D values that correspond exactly to the 3D input? Running the
>realignment on the MoAEpilot fM00223 3D files and this 4D that I created, I
>get 3D r* and 4D r* output that differs in some x-y-z locations only by plus
>or minus 0.125, again the scl_slope setting in the input. Is this just a
>coincidence?
I assume that in both paragraphs above, the issue is that datasets of integer
type have a scaling factor, and for the 3D images, the scaling factor can be
different for each 3D volume, whereas for the 4D image, there must be a
single scaling factor for all the 3D volumes belonging to the 4D image. Also,
even if all the 3D inputs have the same scaling factor, SPM might choose a
different scaling factor for output for a 4D volume.
Because of those issues, one might expect the answers for the 3D and 4D
cases could differ. You could test this by getting SPM to output using floating
point.
>One other 4D note is that SPM seems to be able to effect a trim of the first
>few volumes if I specify a frame filter such as 7:N for input to
>realignment, but normalisation gives an error on any results not generated
>with 1:N. So, I assume that I must first trim any 4D input before using it
>in the pre-processing data stream.
>
>Thanks for any comments on the practical usage of 4D in SPM8.
>
>Kathy Pearson
>CU-Boulder Psychology
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