This bug was fixed by the gcc 4.1.2 patch.

 

Thanks,

 

Matt.

 


From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matt Glasser
Sent: Wednesday, February 06, 2008 5:48 PM
To: [log in to unmask]
Subject: Re: [FSL] Probtrackx Bug +

 

Edit:

 

This bug started happening after I updated the probtrackx to the latest version, so it is not a problem with the script that generated the commandline below (I ran some analysis with that exact commandline on another subject that worked fine).


Thanks,


Matt.

 


From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matt Glasser
Sent: Wednesday, February 06, 2008 5:44 PM
To: [log in to unmask]
Subject: Re: [FSL] Probtrackx Bug +

 

Saad,

 

Also it is not outputting any results, just the log and waytotal.  I thought this was because one of my computers was being unstable, but it occurs on both my machines and the other is rock solid stable.  An example commandline is probtrackx --seed=/media/500GB/data/Macaques/PostMortemMacaque2/data/ROIs/R_Superior_Posterior_1stWhiteMatterVoxelLayer1 --targetmasks=/media/500GB/data/Macaques/PostMortemMacaque2/data/ROIs/R_Targets_List_For_Superior_Posterior_1stWhiteMatterVoxelLayer1.txt -s /media/500GB/data/Macaques/PostMortemMacaque2/data/../data.bedpostX/merged -m /media/500GB/data/Macaques/PostMortemMacaque2/data/../data.bedpostX/nodif_brain_mask.nii.gz --loopcheck --cthr=0.2 --nsteps=2000 --steplength=0.1375 --nsamples=1 --fibthresh=0.05 --randfib --os2t --pd --dir=/media/500GB/data/Macaques/PostMortemMacaque2/data/Results/R_Superior_Posterior_1stWhiteMatterVoxelLayer1_Results_Distance_Corrected --forcedir &

 

Thanks,

 

Matt.

 


From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Saad Jbabdi
Sent: Wednesday, February 06, 2008 9:50 AM
To: [log in to unmask]
Subject: Re: [FSL] Probtrackx Bug +

 

I can't replicate that :-(

Can you email me a copy/paste of the command line you're using?

 

 

 

On 5 Feb 2008, at 18:34, Matt Glasser wrote:

 

Saad,

 

I think this just started happening with the latest patch 4.0.3-1.  I tried it on two separate computers running ubuntu gutsy 64bit (fsl from the hanke packages).  I didn’t do any custom modification or compiling of FDT.  Where did you place the --forcedir option in the commandline?

 

Thanks,

 

Matt.


From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Saad Jbabdi
Sent: Tuesday, February 05, 2008 12:56 PM
To: [log in to unmask]
Subject: Re: [FSL] Probtrackx Bug +

 

Hi Matt

This is strange, I can't replicate this in any of the released versions of FDT since FSL4.0. When I do --forcedir, it does not add a + for me!

 

As for choosing the output file name, it will be in the next patch!

 

Cheers,

Saad.

 

On 4 Feb 2008, at 19:06, Matt Glasser wrote:

 

Hi probtrackx coders,

It seems that the --forcedir switch has recently stopped working in probtrackx, and instead of overwriting old results it is putting the pluses. This breaks my scripts unfortunately. L Can you look into this bug? Also, Tim sent me some code a while back that allowed probtrackx to output a specific file name in path distribution mode a while ago. I was wondering if that ever made it into the FSL releases.

Thanks,

Matt.

 

---------------------------------------------------------------------------

Saad Jbabdi,

Postdoctoral Research Assistant,

Oxford University FMRIB Centre

 

FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK

+44 (0) 1865 222545 (fax 222717)

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---------------------------------------------------------------------------

Saad Jbabdi, 

Postdoctoral Research Assistant,  

Oxford University FMRIB Centre

 

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK

+44 (0) 1865 222545  (fax 222717)

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