Hi,
I'm afraid I'm not very familiar with the workings of SPM at this level.
However, what you'd done looks sensible to me. Is there any sform
or qform information in the nifti image? It is possible that SPM might
use this to determine the order of the slices, whereas FSL just uses the
voxel coordinates.
All the best,
Mark
On 30 Jun 2009, at 08:59, Nico wrote:
> Hi everyone!
>
> We have encountered a rather strange behaviour using “Slice timing“–
> during
> preprocessing - in FSL compared to SPM.
>
> First I tell you what we did.
>
> Overall info:
>
> Linux Version: debian lenny
> FSL Version 4.2.1
> SPM Version 5
> TR: 2,5 sec
> Nr.of Slices: 31
> Measurement: Interleaved – starting with Slice 1 ( 1,3,5 ... 31,
> 2,4,6...30)
>
>
> 1. We converted the raw DICOMs into a 4D Nifti-file
>
> 2. During pre-processing we found a striking difference in the slice
> timing
> operation between FSL and SPM.
>
> 3. Looking at the slice timing specs in detail:
>
>
> i. with FSL we used:
> slicetimer –i raw4dnifti –o output –r 2.5 –ocustom=ST_FILE
> ST_FILE is ascii text with one number per line (1 3 5 etc.).
> Using option “odd” yields exactly the same result.
>
>
> ii. with SPM5 we used:
> spm_slice_timing(P, sliceorder , refslice, timing);
> with:
> nslices = 31; TR = 2.5; TA = TR-TR/nslices;
> timing(2) = TR - TA;
> timing(1) = TA / (nslices -1);
> refslice=31;
> sliceorder=[1:2:31 2:2:31]
> P the volumes from raw4dnifti (fslsplit)
>
> (in FSL and SPM the same raw data and the same TR were entered. Both
> Systems
> used TR/2 as reference)
>
>
> 4. Looking at the results there is a discrete difference between
> these two
> analyzes.
>
> The surprise was that when we _reverse_ the Sliceorder on one System
> (FSL or
> SPM) we can create the result of the other system. Meaning changing
> the
> Sliceorder in SPM (sliceorder=[30:-2:1 31:-2:1]) creates the FSL
> results and
> reversing the file ST_FILE
> (tac ST_FILE > reverse_ST_FILE and using this; ) yields exactly the
> SPM results.
>
>
>
>
> Now the question:
> Did we make any mistakes concerning entering the sliceorder?
> Do you have any idea to explain this discrepancy between SPM and FSL?
>
>
> Cheers,
> Nico
>
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