Hi Jamie,
Three time points should not be a memory problem. You can try to run this on linux. Or you can get a new binary for the mac from our development version with several improvements and fixes including a memory leak that might have caused this. Let me know (you may want to rerun all your bases with the new version then to avoid introducing a bias, it uses cubic interpolation and should produce better results).
Best Martin

"Kawadler, Jamie" <jamie.kawadler.11@ucl.ac.uk> wrote:

Hello,

I have a dataset of patients with 3 time points each. While 2-time point processing works just fine in the longitudinal stream, when I run a base with 3 time points, the process fails and exits with errors.

Please see the output below:

Resolution: 0 S( 256 256 256 ) T( 256 256 256 )

Iteration(f): 1 -- diff. to prev. transform: 0.160049

Iteration(f): 2mri_robust_template(778) malloc: *** mmap(size=262144) failed (error code=12)

*** error: can't allocate region

*** set a breakpoint in malloc_error_break to debug

MRIalloc(256, 256, 256): could not allocate 262144 bytes for 129th slice

Cannot allocate memory

Darwin Jamies-iMac.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64

recon-all -s EB1312_61-66-77_base exited with ERRORS at Wed Sep 26 12:19:11 BST 2012

This is similar to a message on the mailing list from Liz Bowman (30 Jul 2012), in which the response was to get more memory. My command was done on a Mac with 16GB of RAM and ample disk space.

I'd appreciate any help!

Thanks,

Jamie Kawadler
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Sent from my phone, please excuse brevity.