1. It is not contrast enhanced. 2. I am rerunning recon-all after giving it a manually skull stripped image. Hopefully this will work.
So basically did this: recon-all -subjid . -autorecon1 -noskullstrip -notal-check cp T1.mgz brainmask.auto.mgz ln -s brainmask.auto.mgz brainmask.mgz recon-all -subjid . -autorecon2 -autorecon3 On Tue, Feb 26, 2013 at 3:10 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > thanks. I actually meant a tksurfer image, but this might do. Two > questions: > > 1. Is this a contrast-enhanced acquisition? That will make things more > difficult, although we have processed them in the past. > > 2. I think the skull stripping removed some brain tissue, which may be the > source of your large defects. Can you please check it and get back to us? > This also might be due to the contrast enhancement. > > cheers > > Bruce > > > On Tue, 26 Feb 2013, Blessy M wrote: > > I should have send it with an extension. But it is tiff, just as you >> asked. >> >> On Tue, Feb 26, 2013 at 3:03 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Blessy >> >> what format is this? If you don't send it with an extension there >> is no way to know.... >> Bruce >> On Tue, 26 Feb 2013, Blessy M wrote: >> >> Forgot the image. please find attached. >> >> >> On Tue, Feb 26, 2013 at 2:45 PM, Blessy M <bles...@gmail.com> >> wrote: >> I ran this command, and got the attached image >> tkmedit ./ brainmask.mgz lh.inflated.nofix >> >> For some reason tksurfer is not looking good/complete >> tksurfer ./ lh inflated >> >> >> On Tue, Feb 26, 2013 at 11:53 AM, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> wrote: >> you can save a tif of it and post it to the list >> On Tue, 26 Feb 2013, Blessy M wrote: >> >> Yes it is still at defect 32. >> >> The tail of the recon-all.log is as follows: >> >> CORRECTING DEFECT 30 (vertices=18, convex >> hull=22) >> After retessellation of defect 30, euler >> #=-7 (59491,172395,112897) : difference with >> theory >> (-28) = -21 >> >> CORRECTING DEFECT 31 (vertices=244, convex >> hull=142) >> After retessellation of defect 31, euler >> #=-6 (59502,172495,112987) : difference with >> theory >> (-27) = -21 >> >> CORRECTING DEFECT 32 (vertices=44865, >> convex hull=8969) >> >> >> Should I attach the lh.inflated.nofix in a >> separate email to you, Bruce? >> >> >> >> On Tue, Feb 26, 2013 at 10:08 AM, Bruce >> Fischl <fis...@nmr.mgh.harvard.edu> wrote: >> is it still on defect 32? What does >> the tail of the recon-all.log say? And can >> you >> send us an image of the >> lh.inflated.nofix (if it is the lh >> that is running)? >> >> On Tue, 26 Feb 2013, Blessy M wrote: >> >> I verified lh.orig.nofix, and >> it looks fine. But, there has been no new >> files >> created since Saturday >> (2/23/2013). >> >> I am considering stopping the >> process. >> >> I was thinking, I had created a >> skull stripped image, and was giving that >> as >> input to recon-all in the >> command below: >> recon-all -subjid . >> -noskullstrip -autorecon1 -notal-check -autorecon2 >> -autorecon3 >> >> Should -noskullstrip flag be >> after autorecon1? >> >> >> >> On Mon, Feb 25, 2013 at 3:35 >> PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> try looking at the >> lh.inflated.nofix or lh.orig.nofix (or rh, >> whichever >> one is running) and see if >> something is >> dramatically wrong (like >> skull attached to brain, or hemis >> connected, >> etc....) >> On Mon, 25 Feb 2013, >> Blessy M wrote: >> >> Recon is still >> running. I started the process on 2/21/2013. >> Its been >> 4 days. >> >> I ran this command, >> and viewed the aseg file, and that looks >> reasonable >> tkmedit ./ >> brainmask.mgz -aux T1.mgz -surfs -aseg >> >> Currently it is at >> this stage: >> >> Correction of the >> Topology >> Finding true center >> and radius of Spherical Surface...done >> Surface centered at >> (0,0,0) with radius 100.0 in 13 iterations >> marking ambiguous >> vertices... >> 124766 ambiguous >> faces found in tessellation >> segmenting >> defects... >> ...... >> >> 61 defects to be >> corrected >> 0 vertices >> coincident >> ...... >> ...... >> CORRECTING DEFECT >> 31 (vertices=244, convex hull=142) >> After >> retessellation of defect 31, euler #=-6 >> (59502,172495,112987) >> : difference with theory >> (-27) = -21 >> >> CORRECTING DEFECT >> 32 (vertices=44865, convex hull=8969) >> >> >> >> >> >> >> >> >> On Fri, Feb 22, >> 2013 at 5:33 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >> I don't think >> either one of these are errors, just >> warnings >> that occur pretty >> frequently and I >> don't think should >> impact the >> results. Does the recon finish? Do the >> results look >> ok? >> >> On Fri, 22 >> Feb 2013, Blessy M wrote: >> >> >> I am >> getting the bottom two sets of errors while >> doing a >> simple recon-all. >> >> More >> specifically while running this command: >> >> recon-all -subjid . -noskullstrip -autorecon1 >> -notal-check -autorecon2 >> >> -autorecon3 >> >> Has >> someone encountered this kind of errors? Is >> there a >> fix? >> >> 1) >> >> Computing MAP estimate using 2772 samples... >> >> ********************************************** >> IFLAG= >> -1 LINE SEARCH FAILED. SEE DOCUMENTATION >> OF >> ROUTINE MCSRCH ERROR >> RETURN >> OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: >> FUNCTION >> OR GRADIENT ARE >> >> INCORRECT OR INCORRECT TOLERANCESoutof >> QuasiNewtonEMA: >> 011: -log(p) = >> 7296.5 >> tol 0.000010 >> ... >> ... >> >> 2) >> >> unfolding failed - restoring original position >> -------------------- >> 0146: >> dt=13.779160, rms=0.814 (0.000%), neg=0, >> invalid=766 >> >> blurring input image with Gaussian with >> sigma=0.500... >> 0000: >> dt=0.000, rms=0.814, neg=0, invalid=766 >> >> gcamFindOptimalTimeStep: Complete in 101542.133 ms >> iter 0, >> gcam->neg = 801 >> >> >> ...................... >> >> >> unfolding failed - restoring original position >> -------------------- >> 0158: >> dt=13.828393, rms=0.814 (-0.069%), neg=0, >> invalid=766 >> >> blurring input image with Gaussian with >> sigma=0.500... >> 0000: >> dt=0.000, rms=0.814, neg=0, invalid=766 >> >> gcamFindOptimalTimeStep: Complete in 100610.148 ms >> >> >> >> >> >> 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<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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