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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