The process is still running but nothing new written in the last 24 hrs. Excerpts from recon-all.log
...... 77 defects to be corrected 0 vertices coincident reading input surface /home/#########/subjects/./surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... ....... CORRECTING DEFECT 20 (vertices=71, convex hull=55) After retessellation of defect 20, euler #=-3 (58272,166451,108176) : difference with theory (-54) = -51 CORRECTING DEFECT 21 (vertices=17, convex hull=34) After retessellation of defect 21, euler #=-2 (58273,166465,108190) : difference with theory (-53) = -51 CORRECTING DEFECT 22 (vertices=39536, convex hull=7215) Help! On Wed, Feb 27, 2013 at 11:37 AM, Blessy M <bles...@gmail.com> wrote: > > 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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