Dear Paul Macey:
Your script is exactly what I was looking for, and allows me to apply
bias correction onto other anatomical sequences like FLAIR, T2W, and
etc. However I have one question. Can you assume EPI field
inhomogeneity, or distortion, is similar to anatomical sequence?
With regards,
Hedok
Paul Macey wrote:
> Hi Marko
>
> Although I haven't used the old SPM2 bias correction in SPM5, I did
> write a short script to apply the bias correction as determined in the
> SPM5 unified segmentation to images other than the input image (m-file
> attached). This is not what you asked for, but it may be handy for you
> or others. I've used this to correct bias in EPI images - I run the
> SPM5 segment on the mean image, then apply the correction to all the
> images in the series.
>
> Best wishes,
> Paul
>
> Marko Wilke wrote:
>> Dear All,
>>
>> I know, the bias estimation as implemented in the segmentation is
>> superior but I would still like to play around with the command line
>> version that directly estimates the bias in the image as implemented
>> in spm_bias_estimate and spm_bias_apply.
>>
>> It seems that the estimation did not change from spm2 to spm5 but the
>> process works in spm2 and does not in spm5... specifically, if I call
>> spm_bias_estimate, I get an error related to the plotting of results
>> ("vectors must be the same length"), or Matlab crashes completely.
>> Uncommenting the plot still crashes Matlab, so the error seems to be
>> in the mex-file. Using the spm2-dll does not work as the spm_vol
>> syntax changed, and re-compiling the spm5-version also does not
>> succeed, likely due to the inaptness of the operator.
>>
>> My question is, has anyone used spm_bias_estimate in spm5 on a
>> Windows machine? If so, I would appreciate receiving your dll-file to
>> see if it is a local problem.
>>
>> Best regards and thanks in advance,
>> Marko
>>
> ------------------------------------------------------------------------
>
> function cspm_bias_writecorrected( sn_file, P )
> if ~strcmp(spm('ver'),'SPM5')
> msgbox('Function works with SPM5 only.')
> return
> end
> if nargin < 1
> sn_file = spm_select(1,'mat',...
> 'Select spatial normalization parameters (from segment/unified)');
> end
> if nargin < 2
> P = spm_select(Inf,'image',...
> 'Select files to be bias-corrected using sn parameters');
> end
> if iscell(P)
> P = char(P);
> end
>
> sn = load(sn_file);
>
> opts.biascor = 1;
> opts.GM = [0 0 0];
> opts.WM = [0 0 0];
> opts.CSF = [0 0 0];
> opts.cleanup = 0;
>
> % Rename priors as the path will vary according to SPM5 location
> sn.VG(1) = spm_vol( fullfile(spm('dir'),'apriori','grey.nii') );
> sn.VG(2) = spm_vol( fullfile(spm('dir'),'apriori','white.nii') );
> sn.VG(3) = spm_vol( fullfile(spm('dir'),'apriori','csf.nii') );
>
> for m = 1:size(P,1)
> sn.VF = spm_vol(deblank(P(m,:)));
> spm_preproc_write(sn,opts)
> end
>
