These misregistrations are all fairly small, so I don't envisage any
real problems.
Best regards,
-John
On 3 November 2010 12:57, Paloyelis, Yannis <[log in to unmask]> wrote:
> Dear John,
> Thank you very much for your response and your time. The reason the
> discrepancies appeared in the translations was that I was silly! I compared
> the N.mat and N.mat0 after I had manually changed the origin of the axes so
> that it fell on the AC!
> Doing it properly this time, there were no differences in the translations,
> but very small differences in the other columns. I used the script you
> posted (attached below embedded in a loop), and for a group of 30-something
> scans the misregistrations (in mm) for the given voxel (100, 200, 50) for
> each scan are presented below. Given these misregistrations, would you think
> that I should avoid using DARTEL with the DICOM-converted scans (and use
> instead UNC-converted scans in Analyze format that present no
> misregistrations - I try to avoid this because there is no orientation
> information in the files), or would you think that the misregistrations
> below are so small that it wouldn't probably make a difference? (Or am I
> doing something wrong here?)
> Thanks a million for your help!
> Kind regards,
> yannis
> Misregistrations:
> EDU>> M'
> ans =
> 0.0013
> 0.1005
> 0.0011
> 0.0611
> 0.0005
> 0.0016
> 0.0010
> 0.0015
> 0.0975
> 0.0014
> 0.0031
> 0.0000
> 0.0005
> 0.0023
> 0.0817
> 0.0014
> 0.0022
> 0.0473
> 0.0333
> 0.0008
> 0.0011
> 0.0003
> 0.0028
> 0.0664
> 0.0011
> 0.0003
> 0.0020
> 0.0021
> 0.0014
> 0.0016
>
>
> +++++SCRIPT++++++++
> [ConvertedFiles,dirs] = cfg_getfile('FPList', [root],'^D.*\.nii$');
>
> i=100; j=200; k=50; %voxel
>
> scan=1
> for f=1:length(ConvertedFiles)
> display (char(ConvertedFiles(f)))
> N=nifti(char(ConvertedFiles(f)));
> N.mat
> N.mat0
>
>
>
> D=N.mat-N.mat0;
> M(scan)=sqrt(sum((D(1:3,1:4)*[i j k 1]').^2))
>
> scan=scan+1
>
> end
>
>
>
>
> On 2 Nov 2010, at 08:41, John Ashburner wrote:
>
> If these are the mat and mat0 fields, then the only difference I see
> is in the translations (2mm in x, 44mm in y and 1mm in z). If there
> is some form of shearing in the data, I'd expect the rotation and
> zooming part to differ. I'm not sure why the translations differ, but
> don't think this should be a problem for Dartel.
>
> Best regards,
> -John
>
> On 1 November 2010 16:28, Yannis Paloyelis <[log in to unmask]>
> wrote:
>
> Dear John,
>
> I am coming back to this issue as I am not sure I understand how to deal
> with it. I get this warning when displaying with "Display" DICOM-converted
> images (T1-weighted volumes, using the SPM tool -scanner was a General
> Electric SIGNA HDx 3.0T). Comparing the V.mat and V.mat0 for some images
> reveals no difference up to the 4th decimal, whereas for others there is a
> big difference at values in the 4th column (see below for example). My aim
> is to do VBM using DARTEL. I am not sure I understood how to deal with this
> - should I try some other utility to convert the DICOM files (are there any
> you would recommend?). Is it right that I cannot use DARTEL for VBM while
> N.mat and N.mat0 differ like this?
>
>
> Thanks very much for help in advance.
>
> Kind regards,
>
> yannis
>
> ans =
>
> -1.0906 0.0005 0.0846 134.5624
>
> -0.0841 -0.0062 -1.0967 100.3869
>
> 0 1.0938 -0.0063 -153.4530
>
> 0 0 0 1.0000
>
>
> ans =
>
> -1.0906 0.0005 0.0846 132.5624
>
> -0.0841 -0.0062 -1.0967 144.3869
>
> -0.0000 1.0938 -0.0063 -154.4530
>
> 0 0 0 1.0000
>
>
> ---------------------------------------------
> Yannis Paloyelis, BSc (Hons) MSc MSc
> PhD Student
> Office C3.18 (P080)
> MRC Social Genetic and
> Developmental Psychiatry Centre
> Institute of Psychiatry,
> King's College London
> De Crespigny Park
> SE5 8AF London
> Tel. +44-20-7848-5403
> Fax +44-20-7848-0866
>
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