Okay, understood. Thanks again for your help. Best regards, Jake
On Fri, Jul 28, 2017 at 11:20 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > it depends. In this case you want to erase as it creates an incorrect > connection. In others you want to add if there is an incorrect break > On Fri, 28 Jul 2017, Jake Rieke wrote: > > 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 CenterMalcolm Randall >> VA >> Medical Center, 1601 SW Archer Road, Gainesville, FL 32608 >> Phone: 1-352-376-1611 ext. 5249, E-mail: jakeri...@gmail.com >> >> On Thu, Jul 27, 2017 at 1:09 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> 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: >> overlay_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: >> jakeri...@gmail.com >> >> On Wed, Jul 26, 2017 at 8:16 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> >> 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 >> Freesurfer@nmr.mgh.harvard.edu >> 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 . 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