Hi Bruce,
Just chiming in here given that I've worked on a similar project for brad (hi res hippocampus segmentation). essentially we want to use the hires volumetric data to make a refined segmentation of the amygdala. such a segmentation is not really possible to do given the visual integrity of the 1mm data. but, maybe what we can do (as per your email) is make the labels in the .38 volume data, map that to the 1mm data and then compare the reliability of those labels? thanks so much for your help!
aly
On Aug 10, 2009, at 11:01 AM, Bruce Fischl wrote:
Hi Jon,
I would use the 1mm data to create the surfaces then map them to the hires data and do your tracing that way. You can then use the surfaces for various things like inter-subject registration. I'd need more details to give better advice, but generating surfaces from highres data is hard, and usually not necessary.
cheers, Bruce
On Mon, 10 Aug 2009 jentis@nmr.mgh.harvard.edu wrote:
Hi Bruce,
Yes, we have the 1mm data. However, the project is designed to manually trace an ROI based on the increased visibility in the high- res scans. We need to do reliability to test our method of manual segmentation. Perhaps I am misunderstanding, but it seems like using the 1mm surface data would defeat our purpose. Any suggestions? Thanks again!
Best, Jon
can't you get 1mm data to go with your highres data? For many reasons the high resolution data is usually quite poor for generating surface models.
cheers, Bruce On Sun, 9 Aug 2009 jentis@nmr.mgh.harvard.edu wrote:
Hi Freesurfer team, I am trying to get intra-rater reliability statistics on an ROI manually traced twice (blindly). The scans are anisotropic (.38 x .38 x .8 mm) and so I have not run them automatically through the Freesurfer segmentation because they fail after autorecon1. I tried to use the following command but have had problems: mris_anatomical_stats -a ${s}/label/${h}.aparc.annot -f cortical_thickness_stats/${h}_${s}.txt $s $h
It seems this command requires certain data from the autorecon process such as wm.mgz and other surface information that I cannot get because autorecon fails on these types of scans.
I have only traced one hemisphere (the Left) and the ROIs are saved as label files; an example is: /autofs/space/phrenic_007/users/jon/hires_amy/Round_2/HRDEV126/ whole_amygdala.label
Is there another way to get reliability (pixel overlap, total number of pixels, etc.) for two ROIs? Would you suggest another command or is there a way to bypass those requirements for the mri_anatomical_stats command?
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