I have sent the attachment mentioned in the mail below via mail drop. On Thu, Feb 28, 2013 at 4:28 PM, Blessy M <bles...@gmail.com> wrote:
> The skull stripped image using FS did not look very good, I am not sure if > this was the result of skullt stripping or the fact that the volume was > more than 256^3 (and used -cw256). > So skull stripped it manually, and downsampled it (to be within 256^3mm). > > I am attaching the original image (nii format, is that okay?) with this > mail, I could really use some help with this. > > > > On Thu, Feb 28, 2013 at 11:21 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu > > wrote: > >> have you checked the skull stripping? It looked like it might be cutting >> off some brain. If you upload the subject I'll take a look (although we >> will need the volume before skull stripping). Why are you not stripping >> within FS? That might make life easier for you >> >> cheers >> Bruce >> >> p.s. I think this defect is too large - it's about 1/3 of the cortical >> surface >> >> >> On Thu, 28 Feb 2013, Blessy M wrote: >> >> 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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