Hi Matt and Sebastian,
Very cool article, I'm really looking forward to having a good read through that! Thank you for pointing me towards it. The HCP seems like a fantastic project and has sparked my interest.
Regarding scripts, I've found a few references to scripts for the hires data but can't seem to find actually copies/attachments anywhere (one in particular was a correspondence entitled "Measuring cortical thickness with high resolution data"). In addition, do any HCP: Freesurfer pipeline scripts or step-by-step documentations currently exist? The reason I ask is because the fine details are where I'm running into confusion (for example, something like "the requisite FS volume and surface files are brought into the 0.7mm native volume space, and the WM surface position is adjusted based on intensity gradients in the 0.7mm T1w image" makes sense but I'm really not sure how to approach it).
Also thank you very much for pointing that out, Sebastian; I sometimes forget that the 32-bit binaries could cause problems with RAM constrictions. Because I have already performed a great deal of analysis using 5.1, I would assume it wouldn't be possible to compare any high res results obtained with 5.3 to what I've already obtained using the standard 1mm iso res FS pipeline in 5.1? I've read that changing FS versions during analysis can result in quite different cortical thickness values. That being said, I'm definitely willing to give the high-res analysis a shot with 5.3 regardless.
Thanks very much for your help guys and I apologize in advance for anything that might be unclear - I'm still a bit of a newbie.
Cheers,
Dan
On 2013-06-05, at 12:03 PM, Matt Glasser matt@ma-tea.com wrote:
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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