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
>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>
>
>
> ________________________________
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|