Matthew,
Files were provided, you were able to find and fix the problem.
Thanks for providing the replacement binary, which works.
Replying to the list so this doesn't end up appearing as an unresolved problem.
Thanks, again, for your help.
-- bennet
On Tue, Dec 3, 2019 at 11:31 AM Matthew Webster
<[log in to unmask]> wrote:
>
> Hi Bennet,
> Can you tar up your input files and upload to:
>
> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF
>
> So we can test directly?
>
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
> On 3 Dec 2019, at 15:02, Bennet Fauber <[log in to unmask]> wrote:
>
> Hi, Matthew,
>
> Alas, no. We still get the
>
> malloc: can't allocate region
>
> error. Our most recent output is.
>
> $ probtrackx2 -x masks/L_Hippo.nii -l --onewaycondition -c 0.2 -S 2000
> --steplength=0.5 -P 50 --fibthresh=0.01 --distthresh=0.1 --sampvox=0.0
> --xfm=/Users/tadlab/Desktop/0001/preproc.bedpostX/xfms/standard2diff.mat
> --opd --forcedir -s /Users/tadlab/Desktop/0001/preproc.bedpostX/merged
> -m /Users/tadlab/Desktop/0001/preproc.bedpostX/nodif_brain_mask.nii.gz
> --targetmasks=targets.txt --os2t
> Log directory is: logdir
> Running in seedmask mode
> load seeds
> done.
> Load bedpostx samples
> 1_1
> 1_2
> 1_3
> 2_1
> 2_2
> 2_3
>
> nfibres : 2
> nsamples : 50
>
> Done loading samples.
> Volume seeds
> volume 1
>
> time spent tracking: 4 seconds
>
> save results
> probtrackx2(2139,0x10203e5c0) malloc: can't allocate region
> *** mach_vm_map(size=7597060436055379968) failed (error code=3)
> probtrackx2(2139,0x10203e5c0) malloc: *** set a breakpoint in
> malloc_error_break to debug
> libc++abi.dylib: terminating with uncaught exception of type
> std::bad_alloc: std::bad_alloc
> Abort trap: 6
>
>
> I'm sure you know more about this than I do, but code changes aside,
> the main difference is that the older version is a fat binary and
> includes i386 symbols.
>
> If you compile the current version with debugging symbols and make it
> available to me, I believe I have someone here who can help me get you
> a decent backtrace. More than happy to try to help in any way I can.
>
> Please feel free to contact me off-list if that would be of interest.
>
> Thanks, -- bennet
>
>
> On Wed, Nov 27, 2019 at 11:37 AM Matthew Webster
> <[log in to unmask]> wrote:
>
>
> Hello,
> Can you try re-running with latest FSL ( 6.0.3 ) and let me know if this error persists?
>
> Kind Regards
> Matthew
> --------------------------------
> Dr Matthew Webster
> FMRIB Centre
> John Radcliffe Hospital
> University of Oxford
>
> On 16 Nov 2019, at 00:37, Bennet Fauber <[log in to unmask]> wrote:
>
> We have a new Mac running OS X Mojave. We downloaded and installed
> FSL 6.0.1. When we run probtrackx2 we get the following results and
> error messages.
>
> $ probtrackx2_6.0.1 -x masks/L_Hippo.nii -l --onewaycondition \
> -c 0.2 -S 2000 --steplength=0.5 -P 50 --fibthresh=0.01
> --distthresh=0.1 --sampvox=0.0 \
> --xfm=/Users/tadlab/Desktop/0001/preproc.bedpostX/xfms/standard2diff.mat \
> --opd --forcedir -s /Users/tadlab/Desktop/0001/preproc.bedpostX/merged \
> -m /Users/tadlab/Desktop/0001/preproc.bedpostX/nodif_brain_mask.nii.gz \
> --targetmasks=targets.txt --os2t --s2tastext
>
> Log directory is: logdir
> Running in seedmask mode
> load seeds
> done.
> Load bedpostx samples
> 1_1
> 1_2
> 1_3
> 2_1
> 2_2
> 2_3
> nfibres : 2
> nsamples : 50
>
> Done loading samples.
> Volume seeds
> volume 1
> time spent tracking: 4 seconds
> save results
>
> probtrackx2(56904,0x1172335c0) malloc: can't allocate region ***
> mach_vm_map(size=7597060436055379968) failed (error code=3)
>
> probtrackx2(56904,0x1172335c0) malloc: *** set a breakpoint in
> malloc_error_break to debug libc++abi.dylib: terminating with uncaught
> exception of type std::bad_alloc: std::bad_alloc
>
> Abort trap: 6
>
> This error occurs with binaries for both FSL 6.0.1 and 6.0.2, which we
> installed thinking it might resolve the issue.
>
> We copied over the probtrackx2 file from another Mac, also running
> Mojave, both at the same update level, and it runs. Here is
> information about the two binaries, where we renamed the binaries so
> you can see the FSL versions whence they were obtained.
>
> mac-csmonk03:Desktop tadlab$ lipo -info /usr/local/fsl/bin/probtrackx2_509
> Architectures in the fat file: /usr/local/fsl/bin/probtrackx2_509 are:
> i386 x86_64
>
> mac-csmonk03:Desktop tadlab$ lipo -info /usr/local/fsl/bin/probtrackx2_6.0.1
> Non-fat file: /usr/local/fsl/bin/probtrackx2_6.0.1 is architecture: x86_64
>
> Given the size reported -- size=7597060436055379968 -- something is
> seriously wrong with that value.
>
> Please let us know if we can provide additional information.
>
> Similar problems were reported for fslview earlier, and with slicer,
> in case that is of any help.
>
> Subject: fslview error
> Date: Mon, 16 Nov 2015 15:50:07 +0000
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;596f63cd.1511
>
> Subject: FSLView crash
> Date: Thu, 25 Jun 2015 00:40:58 +0100
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;44aa434c.1506
>
> Subject: Error Registration Fieldmap
> Date: Tue, 19 Dec 2017 11:48:37 +0000
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;214eaaba.1712
>
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