Yep, make sure you include that;) Very clever option though, don't you think;);).
Cheers-
Andreas
-----Ursprüngliche Nachricht-----
Von: FSL - FMRIB's Software Library im Auftrag von Scott Kolbe
Gesendet: Do 14.02.2008 00:52
An: [log in to unmask]
Betreff: Re: [FSL] probtrackx problems
okay, okay. i think i gots it. the option -opd wasn't included...
stupid!
s
Scott Kolbe wrote:
> Thanks Matt
> You were right, there was a problem with one of the paths. after i
> changed it the job ran ok but there was no results file saved in the
> output directory. the output options i used were:
>
> --dir=$PWD/BEDPOSTX.bedpostX/tracts/
> --forcedir
>
> has anyone else experienced this behaviour?
>
> cheers
> scott
>
>
>
>
> Matt Glasser wrote:
>> Have you verified that all of your paths and filenames are correct?
>> You can
>> do that by typing the full path and filename after ls.
>>
>> Peace,
>>
>> Matt.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>> Behalf
>> Of SK
>> Sent: Tuesday, February 12, 2008 10:09 PM
>> To: [log in to unmask]
>> Subject: [FSL] probtrackx problems
>>
>> Dear FSL list
>> just trying to run probtrackx but my jobs keep failing. I started
>> trying to run from the GUI but got no love unless i used a single
>> seed voxel. The job failed if I: a) used a mask for seeding, or b)
>> used a termination mask even with single voxel seeding. i then tried
>> from the command line and got the 'exit without doing anything'
>> error. here is the command i entered (each option on a new line):
>> $> probtrackx
>> --seed=~/dmf/BEDPOSTX_test/seed_mask_left
>> --mask2=~/dmf/BEDPOSTX_test/V1_MNI_2mm_left_norm_thresh_45%_mask
>> --mode=twomasks_symm
>> -s ~/dmf/BEDPOSTX_test/BEDPOSTX.bedpostX/merged
>> -m ~/dmf/BEDPOSTX_test/BEDPOSTX.bedpostX/nodif_brain_mask
>> --loopcheck
>> --cthr=0.2
>> --nsteps=2000
>> --steplength=0.5
>> --nsamples=5000
>> -f
>> --stop=~/dmf/BEDPOSTX_test/termination_mask
>> --dir=~/dmf/BEDPOSTX_test/BEDPOSTX.bedpostX/tracts/
>> --forcedir &
>>
>> if anyone has any ideas why this job might keep failing please let me
>> know coz i'm stumped. we are running FSL 4.0 built on SUSE Linux on
>> an SGI Altix.
>> cheers
>> Scott
>>
>>
>
>
--
========================
Scott Kolbe
PhD Candidate
Neuroimaging Group
Howard Florey Institute &
Centre for Neuroscience
University of Melbourne
VIC, Australia, 3010.
ph- +61 3 8344 1887
email - [log in to unmask]
http://www.florey.edu.au/index.php?id=142
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