I had a similar problem with my nifti-images in float format and the
HDW for the same images worked well when converting them to int16. I
never figured out why...
Best,
Michel
> Date: Mon, 29 Jun 2009 21:28:03 +0100
> From: [log in to unmask]
> Subject: Re: [SPM] Two HDW questions
> To: [log in to unmask]
>
> It was the only explanation of why it would suddenly stop working that I
> could think of. I was reasoning that the headers may put the images out
> of alignment with each other, but that does not seem to be the case. I
> don't think that a change in datatype could cause such a problem, but I
> may be wrong. Maybe NaNs have entered into the data. I'm not sure how
> the code deals with them.
>
> I'll be away from the mailing list for a few days, but email me again in
> a week if you haven't figured out the cause of the problem.
>
> Best regards,
> -John
>
> On Mon, 2009-06-29 at 15:07 -0500, Guofan Xu wrote:
> > Thanks for the quick answer. Those N3-correction was done with freesurfer and converted back to nifti format. They looks well in spm5 "display" & "check-reg" functions. Is there any specific head info or field I should check?
> >
> > guofan
> > 6.29
> >
> > >>> John Ashburner <[log in to unmask]> 6/29/2009 3:06 PM >>>
> > It sounds like a file format issue to me, as I'm not sure whether there
> > is a NIfTI compatible version of N3. Use Check Reg to make sure that
> > the bias corrected images are in alignment with each other.
> >
> > Best regards,
> > -John
> >
> >
> > On Mon, 2009-06-29 at 11:53 -0500, Guofan Xu wrote:
> > > Hi, Nikos:
> > > Actually I got the same error from High Dimensional Warping from my data and the results (Jacobians) is NOT good. I used N3-correction for my T1-MPRAGE data and SPM HDW gave me the same complain as you had. Before the N3-correction, HDW runs OK and I got a brain-shaped Jacobian file. I am curious why HDW gave me such error as well.
> > >
> > >
> > > Guofan
> > > 6.29
> > >
> > >
> > > Guofan Xu
> > > Department of Medicine
> > > Geriatrics & Gerontology Section
> > > Veterans Administration Hospital
> > > 2500 Overlook Terrace
> > > Madison, WI 53705
> > >
> > >
> > > >>> Nikos Koutsouleris <[log in to unmask]> 6/29/2009 4:04 AM >>>
> > > Dear John & VBM experts,
> > >
> > > I have two question regarding HDW:
> > >
> > > 1) When running spm_hdw I get the following warning during the differential
> > > bias field correction step :
> > >
> > > Warning: Matrix is singular, close to singular or badly scaled.
> > > Results may be inaccurate. RCOND = NaN.
> > > > In spm_hdw>bias_correction at 208
> > > In spm_hdw>run_warping at 30
> > > In spm_hdw at 14
> > > In spm_jobman>run_struct1 at 1585
> > > In spm_jobman>run_struct1 at 1595
> > > In spm_jobman>run_struct1 at 1595
> > > In spm_jobman>run_job at 480
> > > In spm_jobman at 89
> > >
> > > is this a serious problem that may affect my results or can I safely ignore it.
> > >
> > > 2) Is there any possibility to parallelize spm_warp.c by means of OpenMP,
> > > e.g. using a simple #pragma omp parallel directive at some for loop in the
> > > source code?
> > >
> > > Any help would be greatly appreciated!
> > >
> > > Best,
> > >
> > > Nikos
> > >
> --
> John Ashburner <[log in to unmask]>
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