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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