Hi Theodor,
I have not managed to replicate any problems with the datasets you sent,
bedpostX runs fine. I agree with Matt's suggestion, do you also have
problems when you run bedpostx on a desktop or they only appear when
running it on a cluster?
Cheers,
Stam
> Are you sure your hardware is stable? You could try running mprime to
> see.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Theodor R?ber
> Sent: Friday, May 27, 2011 7:19 AM
> To: [log in to unmask]
> Subject: Re: [FSL] problem wit bedpostx
>
> 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
>
>
|