Thanks, Bruce and Douglas! Looking at the surface prior to the topology correction step has been very helpful. I can see the region you pointed out - where the wm.mgz connects to the body of the wm, disconnects, and then reconnects at a different spot. I'm having some trouble implementing the manual edits to the wm.mgz. Part of the problem is that I'm still training my eye to differentiate GM and WM (especially in cases with thin tracts or partial voluming), but this gives me a great place to start.
I'm wondering, in general, is the idea to erase or add voxels in the wm.mgz where the defects are located? In other words, defects can be interpreted as areas of misclassified as WM? In this case, it seems that I need to focus on deleting voxels in the wm.mgz that are incorrectly segmented. Thanks, Jake Biomedical Engineer, Brain Rehabilitation Research Center Malcolm Randall VA Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 Phone: 1-352-376-1611 ext. 5249, E-mail: [email protected] On Thu, Jul 27, 2017 at 1:09 PM, Bruce Fischl <[email protected]> wrote: > Hi Jake > > there are voxels like 173, 112, 122 that are incorrectly segmented as wm > (that is, they have a value >=5 in the wm.mgz) that connect two adjenct > gyri. You can either change the intensity thresholds in mri_segment, or > manually erase some of them. The best way to see this is to look at the > surface prior to topology correction, and color it with defect numbers so > you can see where the defects are. Something like: > > cd $SUBJECTS_DIR/<subject id>/mri > freeview -v brain.mgz wm.mgz:colormap=heat:heatscale=1,100 \ > -f ../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels:overl > ay_threshold=1,255:edgecolor=overlay \ > -slice 172 123 134 > > > if you page through a few axial slices you will see that the wm.mgz is > connected to the body of the wm in slice 109, disconnecs in 110, then > reconnects to a different part in 115, which should never happen > > cheers > Bruce > On Thu, 27 Jul 2017, Jake Rieke wrote: > > Hi Bruce, >> >> Thanks for the response. I just uploaded the subject using the ftp file >> exchange. The issue is visible in the region close to voxel coordinate >> [172, >> 123 ,134]. the missing gyrus is capped between coronal slice 141 to 118. I >> forgot to mention in my first message that we used a T2 to improve pial >> surface after initial running with just the T1. >> >> Thanks again >> Jake >> >> Biomedical Engineer, Brain Rehabilitation Research CenterMalcolm Randall >> VA >> >> Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 >> Phone: 1-352-376-1611 ext. 5249, E-mail: [email protected] >> >> On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl <[email protected] >> > >> wrote: >> Hi Jake >> >> usually that means that there is a topology defect that is being >> incorrectly fixed. If you upload the subject and point us at the >> voxel >> coords we will take a look >> >> cheers >> Bruce >> >> On Wed, 26 Jul 2017, Jake Rieke wrote: >> >> > Hello surfers, >> > >> > I'm attempting to extend white and pial surfaces to encompass >> an >> > unrecognized gyrus. The wm.mgz seems include the WM tissue, >> but the white >> > surface does not extend to the WM boundary. I thought this >> might be related >> > to an intensity normalization error and tried using control >> points, but that >> > did not make a big difference in the resulting surfaces. I've >> attached >> > pictures to better illustrate the problem. Thanks in advance >> for your help! >> > >> > Best regards, >> > Jake >> > >> > >> > >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The 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. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The 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. > >
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