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Hi, I can think of two possible reasons for getting this error: 1) You are out of memory 2) Since you have been interpolating your data, did you interpolate the brain mask as well or you obtained a new one by running bet on the interpolated data? If you followed the former approach that can cause problems, you should try the latter one. Cheers, Stam On 11 Nov 2010, at 16:10, shaza zaghlool wrote: > Hi FSL users, > After running the commands below, I got 20 iterations of probtrackx finishing successfully and producing the logdir+ dir each time, but then I started getting this error: > > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > Aborted > > All my masks were created the same way, and have the same resolution, same everything. So I'm not sure why that started happening after the previous ones were working. > > Any suggestions? > Thanks > > On Tue, Nov 9, 2010 at 1:08 PM, shaza zaghlool <[log in to unmask]> wrote: > Hi Matt, > Thank you very much for your response. > My command line is: > > FILES=$(ls LABEL*.nii.gz) > for l1 in $FILES; do > for l2 in $FILES; do > echo $l1 > targetmaskt.txt > probtrackx -s bedpost.bedpostx/merged -m bedpost.bedpostX/nodif_brain_mask.nii.gz -x $l2 --targetmasks=targetmasks.txt --s2tastext --os2t > echo "Tracing $l2 to $l1" > done > done > > Thanks again, > > On Tue, Nov 9, 2010 at 12:57 PM, Matt Glasser <[log in to unmask]> wrote: > Almost 3500 voxels will take a while to run, so I would just be patient. You can post your commandline arguments for probtrackx if you want me to check for any other potential issue. > > > Peace, > > > Matt. > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of shaza zaghlool > Sent: Tuesday, November 09, 2010 11:38 AM > > > To: [log in to unmask] > Subject: Re: [FSL] running probtrackx > > > > > I'm not using a virtual machine. Its a Ubutu OS. > > > > > > On Tue, Nov 9, 2010 at 12:21 PM, shaza zaghlool <[log in to unmask]> wrote: > > Ok I got 3493 36568.089844 when I ran "fslstats -V" on my mask. > > Thanks alot > > Shaza > > On Tue, Nov 9, 2010 at 12:18 PM, Matt Glasser <[log in to unmask]> wrote: > > To find the number of voxels in the mask you can do fslstats <mask> -V. Are you running this in a VM or something like that? > > > Peace, > > > Matt. > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of shaza zaghlool > Sent: Tuesday, November 09, 2010 11:16 AM > > > To: [log in to unmask] > Subject: Re: [FSL] running probtrackx > > > The problem is my original data has high resolution 1x1x3. So that's why I downsampled it to 2x2x2. I'm not sure exactly how many voxels are in my mask file but its a 128x128x67 file with a very tiny mask, I would say less than 5% of that volume. > > On Tue, Nov 9, 2010 at 11:55 AM, Matt Glasser <[log in to unmask]> wrote: > > It would be better to just use the original data and not upsample and then downsample, but that is not the cause of the long time that probtrackx is taking. How many voxels are in your seed mask and what kind of computer are you running this on? > > > Peace, > > > Matt. > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of shaza zaghlool > Sent: Tuesday, November 09, 2010 10:40 AM > > > To: [log in to unmask] > > Subject: Re: [FSL] running probtrackx > > > Hi Matt, > > I downsampled my data to 2x2x2 mm and I used the default settings but it's still going on forever. Is log euclidean downsampling considered as bad as interpolation? > > Thanks > > On Tue, Nov 9, 2010 at 11:30 AM, Matt Glasser <[log in to unmask]> wrote: > > The time it takes depends on the step size, number of voxels in the seed mask, number of samples you send out per voxel, and the single threaded performance of your hardware. If you are running probtrackx on interpolated data it is going to take 8x as long as it should. > > > Peace, > > > Matt. > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of shaza zaghlool > Sent: Tuesday, November 09, 2010 10:23 AM > To: [log in to unmask] > Subject: [FSL] running probtrackx > > > Hello FSL users, > > Can someone tell me how long running probtrackx between a mask and target mask should normally take. For some reason, its not appearing to converge on my machine. What are possible sources of error? > > Thanks, > > > > > > >