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, AustraliaThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.