Dear Bruce and the FS team,

Thank you - we managed to resolve the issue. As mentioned, we are using  “HiResRecon” to process our 0.7mm isotropic data. The attached image on the right shows the result of a control subject after the downsampling pipeline. This GM/WM segmentation is excellent and required very little manual editing. However the image on the left displays the WM/GM segmentation after completion of the high resolution pipeline. The segmentation is quite inaccurate in many areas. Your advice on how to improve this would be greatly appreciated.

Many thanks.

Kind regards,
Megha Kaushik
Save Sight Institute, Sydney

Inline image 2


On Mon, Jan 20, 2014 at 1:05 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Megha

have you tried freeview? How much ram do you have on this machine? Did you try it on another machine? It might just be running out of memory. Can you load the individual surfaces?

cheers
Bruce

 On Sat, 18 Jan 2014, Megha K. wrote:

Dear Nick and the Freesurfer team,

We are following the pipeline “HiResRecon” to process our 0.7mm isotropic
data. The pipeline completed without error but we cannot visualize the
Grey/White matter segmentation using "-surfs”. The error messages is shown
below:

TM:~ Timwang$ tkmedit hires_3 brainmask.mgz -surfs
Converting main surface: 100% done.       
Converting main surface: 100% done.       
Converting pial surface: 100% done.       
Converting main surface: 100% done.       
Converting main surface: 100% done.       
Converting pial surface: 100% done.       
tkmedit.bin(7641,0xa0a8d1a8) malloc: *** mach_vm_map(size=8388608) failed
(error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

We would greatly appreciate your help on how we can visualize the GM/WM
segmentation result of the HiResRecon pipeline.

Many thanks,

Megha Kaushik
Save Sight Institute
Sydney, Australia






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