Yes, but do these errors show up in the cross sectional data, in the base or in the longitudinal data (or all?)? Does it look good in the base?
I'd suggest more skull strip where the pail grabs dura. On Jun 28, 2013, at 11:26 AM, Jonathan Holt <whats...@umich.edu> wrote: > Martin, > > this is longitudinal processing, would you recommend a more aggressive or > less aggressive skull strip? > > Bruce, > > I've not seen this issue on more than a handful of subjects. They're ALS, but > I dont think that is the cause behind this. I'm unfamiliar with bias fields, > but it's more likely than pathology. > > As for control points, there are no more than 5-7 voxels in that area over > the span of 30 slices. Should I simply add to those? > On Jun 28, 2013, at 11:19 AM, Martin Reuter wrote: > >> Hi Jonathan, >> >> is this in cross sectional processing or in longitudinal? >> >> One thing I notice is significant motion artifacts (ringing), which seem to >> lead to underestimation of WM, also you could fine tune the skull strip. >> >> Best, Martin >> >> On Jun 28, 2013, at 10:19 AM, Jonathan Holt <whats...@umich.edu> wrote: >> >>> Hi all, >>> >>> I'm having a bit of trouble with one particular subject for which we brains >>> for 4-5 different time points. The pial surface is consistently misplaced >>> in the same area, see attached main/aux volume images. I'm hesitant to >>> manually replace the white matter myself as I fear it wouldn't be as >>> accurate. Suggestions on other methods to fix this? >>> >>> The problem is always in the LH temporal right around the lateral inferior >>> ventricle and the fusiform and other subcortical structures. >>> >>> >>> <Screen Shot 2013-06-28 at 10.18.59 AM.png><Screen Shot 2013-06-28 at >>> 10.14.50 AM.png>_______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> --------------------------------- >> Dr. Martin Reuter >> Assistant in Neuroscience - Massachusetts General Hospital >> Instructor in Neurology - Harvard Medical School >> MGH / HMS / MIT >> >> A.A.Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, MA 02129 >> >> Phone: +1-617-724-5652 >> Email: >> mreu...@nmr.mgh.harvard.edu >> reu...@mit.edu >> Web : http://reuter.mit.edu >> >> >> 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. >> > --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu
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