[Freesurfer] repost - large-scale reconstruction errors

Any suggestions on how to fix these two types of problems? thanks, Nicole -- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia, PA 19104 Lab phone: 215-746-4371 ___ Freesurfer mailing list Freesurfer@nmr.m

Re: [Freesurfer] repost - large-scale reconstruction errors

examples we will take a look. What version as you > running? Have you checked the accuracy of the talairach.xfm? > > Cheers > Bruce > > > > On Jun 8, 2012, at 11:19 AM, Nicole Senecal > wrote: > > > Hi, > > > > In reconstructing some normal adult MP

[Freesurfer] aseg inaccuracy in cortex

this boundary correctly. As long as the surfaces are correct, and my primary interest will be cortical thickness, do I need to worry about these inaccuracies in the aseg? Is checking the aseg primarily done for ensuring accuracy in subcortical structures rather than in cortex? thanks, Nicole -- N

[Freesurfer] Scripting with fs 5.1 vs 5.0

fer5-1/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /jet/kable/CorticalThickness/Subjects MNI_DIR /usr/local/freesurfer5-1/mni FSL_DIR /usr/local/fsl thanks, Nicole -- Nicole Senecal Neuroscience Graduate Group Kable Lab 3720 Walnut St., Room C37 Philadelphia,

Re: [Freesurfer] wm problems

#x27;t follow the wm.mgz it means there was a > topological defect that was corrected in that region. You can find it and > fix it be editing the wm. If you can't find it, upload it and send us the > coords you are looking at and we'll find it and show you. > > cheers >

[Freesurfer] Large part of brain missing from wm.mgz and surfs

Hi all, My lab is just starting to use Freesurfer, and are finding that a lot of our recon-all jobs are needing a fair amount of editing. We've run into a problem that we can't figure out how to address - on several of our brains, a large chunk (up to 2/3 of the brain) is missing from the wm.mgz f