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
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?
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 ... ...
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
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.eduwrote:
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?
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 ... ...
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/**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.
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 msThe 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 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.eduwrote:
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 asimple 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 ROUTINEMCSRCH 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 msThe 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/**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.
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.
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.eduwrote:
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 looksreasonable 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 whiledoing 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? Isthere a fix?
1) Computing MAP estimate using 2772 samples... ********************************************** IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATIONOF 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 theperson 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.
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 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.eduwrote:
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 hasbeen 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 wasgiving 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 on2/21/2013. Its been 4 days.
I ran this command, and viewed the aseg file, andthat 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 SphericalSurface...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, convexhull=142) After retessellation of defect 31, euler #=-6 (59502,172495,112987) : difference with theory (-27) = -21
CORRECTING DEFECT 32 (vertices=44865, convexhull=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 oferrors while doing a simple recon-all.
More specifically while running thiscommand: recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2 -autorecon3
Has someone encountered this kind oferrors? Is there a fix?
1) Computing MAP estimate using 2772samples... ********************************
IFLAG= -1 LINE SEARCH FAILED. SEEDOCUMENTATION 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 - restoringoriginal 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 originalposition -------------------- 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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freesurfer@nmr.mgh.harvard.edu
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Blessy M -
Bruce Fischl