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 blessam@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 <fischl@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 <fischl@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 <fischl@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 <fischl@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 . 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.
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 fischl@nmr.mgh.harvard.eduwrote:
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 blessam@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 <fischl@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 separateemail to you, Bruce?
On Tue, Feb 26, 2013 at 10:08 AM, Bruce Fischl <fischl@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 looksfine. 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 skullstripped 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 afterautorecon1?
On Mon, Feb 25, 2013 at 3:35 PM, BruceFischl fischl@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. Istarted the process on 2/21/2013. Its been 4 days.
I ran this command, and viewedthe 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 radiusof 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 5:33PM, Bruce Fischl fischl@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 thebottom two sets of errors while doing a simple recon-all.
More specificallywhile running this command: recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2 -autorecon3
Has someoneencountered this kind of errors? Is there a fix?
1) Computing MAPestimate using 2772 samples...
IFLAG= -1 LINESEARCH 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-mailis 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.
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 fischl@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 <blessam@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 <fischl@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 <fischl@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 <fischl@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 <fischl@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 . 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.
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 fischl@nmr.mgh.harvard.eduwrote:
thanks. I actually meant a tksurfer image, but this might do. Two questions:
- Is this a contrast-enhanced acquisition? That will make things more
difficult, although we have processed them in the past.
- 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 fischl@nmr.mgh.harvard.edu wrote: Hi Blessy
what format is this? If you don't send it with an extension thereis 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 <blessam@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 <fischl@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, convexhull=22) After retessellation of defect 30, euler #=-7 (59491,172395,112897) : difference with theory (-28) = -21
CORRECTING DEFECT 31 (vertices=244, convexhull=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 aseparate email to you, Bruce?
On Tue, Feb 26, 2013 at 10:08 AM, BruceFischl fischl@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, andit looks fine. But, there has been no new files created since Saturday (2/23/2013).
I am considering stopping theprocess.
I was thinking, I had created askull 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 beafter autorecon1?
On Mon, Feb 25, 2013 at 3:35PM, Bruce Fischl fischl@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 stillrunning. 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 atthis stage:
Correction of theTopology 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 becorrected 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 DEFECT32 (vertices=44865, convex hull=8969)
On Fri, Feb 22,2013 at 5:33 PM, Bruce Fischl fischl@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, 22Feb 2013, Blessy M wrote:
I amgetting the bottom two sets of errors while doing a simple recon-all.
Morespecifically while running this command:
recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2
-autorecon3
Hassomeone 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 inthis 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/**compliancelinehttp://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.
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 blessam@gmail.com wrote:
It is not contrast enhanced.
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 fischl@nmr.mgh.harvard.eduwrote:
thanks. I actually meant a tksurfer image, but this might do. Two questions:
- Is this a contrast-enhanced acquisition? That will make things more
difficult, although we have processed them in the past.
- 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 < fischl@nmr.mgh.harvard.edu> wrote: Hi Blessy
what format is this? If you don't send it with an extension thereis 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 <blessam@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 <fischl@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 asfollows:
CORRECTING DEFECT 30 (vertices=18, convexhull=22) After retessellation of defect 30, euler #=-7 (59491,172395,112897) : difference with theory (-28) = -21
CORRECTING DEFECT 31 (vertices=244, convexhull=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 aseparate email to you, Bruce?
On Tue, Feb 26, 2013 at 10:08 AM, BruceFischl fischl@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, andit looks fine. But, there has been no new files created since Saturday (2/23/2013).
I am considering stopping theprocess.
I was thinking, I had createda 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 beafter autorecon1?
On Mon, Feb 25, 2013 at 3:35PM, Bruce Fischl fischl@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 stillrunning. I started the process on 2/21/2013. Its been 4 days.
I ran thiscommand, and viewed the aseg file, and that looks reasonable tkmedit ./ brainmask.mgz -aux T1.mgz -surfs -aseg
Currently it is atthis stage:
Correction of theTopology 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 becorrected 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 DEFECT32 (vertices=44865, convex hull=8969)
On Fri, Feb 22,2013 at 5:33 PM, Bruce Fischl fischl@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, 22Feb 2013, Blessy M wrote:
I amgetting the bottom two sets of errors while doing a simple recon-all.
Morespecifically while running this command:
recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2
-autorecon3
Hassomeone 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
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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 blessam@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 <fischl@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 <fischl@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 <blessam@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 <fischl@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 <fischl@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 <fischl@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 <fischl@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 . 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.
freesurfer@nmr.mgh.harvard.edu
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Blessy M -
Bruce Fischl