I don't think FreeSurfer can handle greater than 1mm data for most of the processing. You can adjust the surfaces using the highres data though. There is are some scripts floating around the list to do that and that is the procedure we used in the HCP pipelines for 0.7mm isotropic data. It is described here:
http://www.sciencedirect.com/science/article/pii/S1053811913005053
I would be interested to know how it works on 0.375 isotropic data, as Bruce has had concerns that laminar myeloarchitecture might get in the way as one gets to resolutions that are high enough to resolve it.
Peace,
Matt.
On 6/5/13 12:22 PM, "Daniel LaFreniere" lafreniere.dj@gmail.com wrote:
Dear Freesurfer Experts,
I'm currently in the middle of processing high resolution MRI through the standard FS pipeline. I've recently read a very interesting article and wanted to attempt a high resolution protocol for a bit of a side project
- we initially obtained an iso resolution of 0.375mm so I might as well
try and make use of it and learn something along the way!
However, I'm starting to run into issues straight from the get-go during -autorecon1. The flag I use is as follows:
recon-all -autorecon1 -mprage -hires -nuiterations 10 -subjid fom04_hires2
Often I use -washu_mprage (dark GM) and -nuiterations closer to 50 since it doesn't seem to hurt anything (the hires protocol takes much longer so I've reduced to 10-20).
After -nuiterations finishes running, I suddenly get the following error:
Writing to ./tmp.mri_nu_correct.mni.902/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.902/nu20.mnc ./tmp.mri_nu_correct.mni.902/nu20.mnc mul 1.33669825436408977556 mris_calc(5163) malloc: *** mmap(size=864002048) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug mris_calc: virtual memory exhausted. Cannot allocate memory Darwin dhcp-10-23-184-237.capitalhealth.ca 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64
recon-all -s fom04_hires2 exited with ERRORS at Wed Jun 5 10:42:36 MDT 2013
For reference, I've added the more detailed recon-all log as well. I'm running a Macbook Pro, OS X 10.8 with 8GB of RAM/2.9 GHz with FS version 5.1.0. I've also been keeping my eye on the Activity Monitor and continuously purge inactive memory as freesurfer runs. I've even had the program crash when I'm sitting at 5 GB of unused memory with a VM size readout of about 420 GB. I can't seem to figure out what's happening but have a feeling that I just need a much more powerful computer to process the 0.375mm voxels. Any help, suggestions, or insight would be greatly appreciated.
Thank you very much for your time,
Dan
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