Hi Stam,
thanks a lot for your help! I have uploaded the
bedpostx-output from three exemplary subjects to the
FMRIB-server.
The reference number is: 393016.
For one of the subjects (6687^20110411), bedpostx has
finished successfully. For the other two (4738^20110404
and 3564^20080526), it apparently has stopped at different
stages.
As I mentioned, the errors we get running bedpostx vary.
Approx. every third time we run bedpostx, it
works properly. If we run one subject twice, it sometimes
works the second time.
Any input is greatly appreciated!
Best,
Theodor
On Thu, 26 May 2011 08:11:51 +0100
Stamatios Sotiropoulos <[log in to unmask]> wrote:
> Hi Theodor,
>
> Can you please upload one of the problematic datasets
>(including bvecs,bvals and brain mask) using
>
> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
>
> and let me know the reference number?
>
> Stam
>
>
>
> ----- Original Message ----- From: "Theodor R?ber"
><[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Thursday, May 26, 2011 1:15 AM
> Subject: Re: [FSL] problem wit bedpostx
>
>
> Hi Stam,
>
> thanks a lot for your answer!
>
> We use FSL 4.1.8
>
> Best,
>
> Theodor
>
>
> ------------------------------
>
> Date: Wed, 25 May 2011 21:46:59 +0100
>From: Stamatios Sotiropoulos <[log in to unmask]>
> Subject: Re: problem wit bedpostx
>
> Hi Theodor,
>
> which FSL version you are using?
>
> Stam
>
>
> ------------------------------
>
> Dear FSL-experts,
>
> We have a problem running bedpostx which causes the
> nodif_brain_mask and the mean/merged volumina
> (mean_f1samples.) to be in a different format. The
> nodif_brain_mask is always correct and binarized but
>there
> are a random number of slices missing in the mean/merged
> volumina (i.e. between 0-60 out of 72 slices). In
>approx.
> a third of the subjects, zero slices are missing and
> everything is fine.
>
> Running > grep ror * < in the logs/ directory we get the
> attached output (the number of lines varies between
> subjects and depends on the number of slices missing).
>
> The bedpostx is parallelised on our SGE-capable system.
>
> Do you have any idea what is going on here?
>
> Your help would be greatly appreciated!
>
> Best,
>
> Theodor
>
>
> Output of two exemplary subjects:
>
> Subject 1:
> bedpostx.e329.1:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.12:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.13:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.14:Logic error:- detected by Newmat:
> incompatible dimensions
> bedpostx.e329.15:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.16:Logic error:- detected by Newmat:
> incompatible dimensions
> bedpostx.e329.19:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.2:Logic error:- detected by Newmat:
> incompatible dimensions
> bedpostx.e329.20:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.21:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.23:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.25:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.26:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.27:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.28:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.31:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.32:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.33:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.34:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.36:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.37:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.38:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.39:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.4:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.40:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.44:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.45:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.46:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.47:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.48:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.5:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.50:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.51:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.52:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.53:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.54:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.55:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.56:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.57:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.58:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.59:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.6:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.60:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.61:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.62:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.63:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.64:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.65:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.66:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.67:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.68:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.69:Logic error:- detected by Newmat: index
> error: requested indices = 1, 1
> bedpostx.e329.8:Logic error:- detected by Newmat:
> incompatible dimensions
> bedpostx.e329.9:Logic error:- detected by Newmat:
> incompatible dimensions
>
> Subject 2:
> bedpostx.e299.14:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.15:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.16:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.17:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.18:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.22:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.23:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.24:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.25:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.26:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.29:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.30:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.31:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.32:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.33:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.34:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.35:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.36:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.37:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.38:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.39:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.40:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.41:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.42:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.43:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.44:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.45:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.46:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.47:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.48:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.49:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.50:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.51:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.52:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.53:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.54:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.55:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.56:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.57:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.58:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.59:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.60:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.61:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.62:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.63:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.64:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.65:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.66:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.67:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.68:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.69:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.70:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.71:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.72:Logic error:- detected by Newmat: index
> error: requested index = 1
> bedpostx.e299.8:Logic error:- detected by Newmat: index
> error: requested index = 1
===================
Theodor Rüber
Remigiusplatz 1
53111 Bonn
Tel.: 0228/24005219
|