Hi Saad,
Thanks for coming back to me, and sorry for my late reply, I was out of
office the last days...
I just checked and tried it with the binary nodif_brain_mask file and now it
is running as usual!
Thank you so much for the fast and very helpful reply!!!
Best,
Jenny
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Saad Jbabdi
Sent: Wednesday, August 25, 2010 6:18 PM
To: [log in to unmask]
Subject: Re: [FSL] Problem BEDPOSTX
Hi - I think it might be because your brain mask is not binarised, with some
values that are between 0 and 0.5.
Can you check if this is the case, and if it works when you binarise it
(fslmaths -bin) ?
Thanks,
Saad.
On 25 Aug 2010, at 15:24, Jennifer Arnold wrote:
> Hallo,
>
> I have problems running bedpostx :
> Within short time (seconds to minutes) I get the following reaction
>
> Making bedpostx directory structure
> Queuing preprocessing stages
> Queuing parallel processing stage
> slice 62 has already been processed
> slice 63 has already been processed
> 2 slices processed
> Queuing post processing stage
> Done!
>
>
> Leaving me with a diff_slices folder and all of the bedpostx.e14188.*
files have the following error message:
>
> An exception has been thrown
> Logic error:- detected by Newmat: index error: requested indices = 1, 1019
>
> MatrixType = Rect # Rows = 34; # Cols = 1018
>
> I also saw that the same problem was posted before and the sugestion that
the bvals and bvecs files would content non-ascii characters, therefore I
checked that:
>
> bash-3.2$ cat -v bvals
> 0.0000000e+00 9.0000000e+02 9.0000000e+02 9.0000000e+02
9.0000000e+02 9.0000000e+02 9.0000000e+02 9.0000000e+02
9.0000000e+02 9.0000000e+02 0.0000000e+00 9.0000000e+02
9.0000000e+02 9.0000000e+02 9.0000000e+02 9.0000000e+02
9.0000000e+02 9.0000000e+02 9.0000000e+02 9.0000000e+02
0.0000000e+00 9.0000000e+02 9.0000000e+02 9.0000000e+02
9.0000000e+02 9.0000000e+02 9.0000000e+02 9.0000000e+02
9.0000000e+02 9.0000000e+02 0.0000000e+00 9.0000000e+02
9.0000000e+02 9.0000000e+02
>
> bash-3.2$ cat -v bvecs
> 0.0000000e+00 4.1803260e-02 -6.7971874e-01 -1.6293473e-01
4.4245684e-01 8.8350599e-01 7.5264137e-01 -3.6808750e-01
5.4017807e-01 9.5086854e-01 0.0000000e+00 7.9858833e-02
7.3773570e-01 -7.2714222e-02 2.9239537e-01 -3.0576150e-01
7.6231974e-01 7.7603520e-01 8.3881219e-01 -1.9101860e-01
0.0000000e+00 2.8655300e-01 -5.3325904e-01 4.1634474e-01
4.9560199e-01 9.4097418e-01 1.4337158e-01 9.6956252e-01
9.0627055e-02 -5.8443841e-01 0.0000000e+00 5.2189911e-01
7.1624621e-01 -4.0842131e-01
> 0.0000000e+00 -9.9404996e-01 -6.6954489e-01 -5.3095446e-01
8.9496600e-02 2.0529976e-01 -6.2578519e-01 3.0542676e-01
-6.2879201e-01 -4.9161109e-02 0.0000000e+00 -7.1734030e-01
6.4263258e-01 -9.3119873e-02 -9.1633063e-01 -8.3759738e-01
2.9443999e-01 -2.3148905e-01 -4.9278888e-01 -9.0937771e-01
0.0000000e+00 -3.8361096e-01 -1.2295929e-01 6.0051497e-01
-8.5563937e-01 3.3091235e-01 -8.1055683e-01 -1.8352598e-01
3.5702919e-01 -5.1402651e-01 0.0000000e+00 -6.2746839e-01
-2.0504897e-01 -9.1334819e-01
> 0.0000000e+00 1.1108279e-01 -2.9762553e-01 8.2958200e-01
8.8856943e-01 -4.1572194e-01 -2.0202168e-01 8.7502602e-01
5.5632268e-01 2.9830818e-01 0.0000000e+00 -6.9132797e-01
-2.0680765e-01 9.9019482e-01 -2.7559798e-01 4.5392912e-01
5.7247643e-01 -5.8287026e-01 2.2656347e-01 -3.7101911e-01
0.0000000e+00 8.7537739e-01 8.3364276e-01 6.8104082e-01
1.4919760e-01 5.3313956e-02 5.6686075e-01 -1.5143777e-01
9.2729308e-01 6.2608807e-01 0.0000000e+00 -5.7688268e-01
6.6286554e-01 9.9110994e-03
> bash-3.2$
>
> It looks fine to me. Do you have any suggestions what to do?
>
> Thank you in advance very much!
> Best regards,
> Jennifer
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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