Hi Megha

yes, the segmentation is currently designed for 1mm. I would use the downsampling, run it through recon-all, then do a final deformation on the original (highres) volume. That pipeline seems to work well, and I believe is what the Wash U-MN HCP does.

cheers
Bruce

On Thu, 30 Jan 2014, Megha K. wrote:

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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