Re: [Freesurfer] mris_register problem
how much? Maybe we should expand the default range? I thought it was already pretty broad, but I haven't looked at it in a long time Glad to hear it worked out cheers Bruce On Tue, 18 Sep 2018, Chris Adamson wrote: External Email - Use Caution Thanks Bruce. I had to increase the angular search range in the affine part to get it to work. Cheers, Chris. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Monday, 17 September 2018 11:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_register problem Hi Chris you need to give us more information. What commands did you run? What was their output? Also, if you can send images of what you think is incorrect that might also be helpful cheers Bruce On Mon, 17 Sep 2018, Chris Adamson wrote: > > External Email - Use Caution > > Freesurfer experts, > > > > I’m having an issue with projecting labels from an atlas to a subject. I have a static annot file on > the atlas that I want to paint onto my subject. The pipeline I have performed is to mris_register my > subject to the atlas and then mri_surf2surf on the annot file using the registered spherical > surfaces. > > > > The labels, when painted, are incorrectly oriented. How can I debug the output of the registration > to check if the registration is working? I assume the registration works in the 2D parameterised > space, can I extract parameterised versions of the curvature maps at each iteration of the > registration. > > > > The strange thing is that when I view the spherical surfaces in freeview with the overlaid curvature > maps they look in alignment prior to registration, but using this unregistered sphere still puts the > labels in an incorrect orientation. So it appears as if there is some rotation that is being done > internally that isn’t shown in freeview. > > > > Please advise, > > > > Chris. > > > > Dr Chris Adamson > > Senior Research Officer > > Developmental Imaging, Clinical Sciences > > > > Murdoch Childrens Research Institute > > The Royal Children’s Hospital > > Flemington Road, Parkville, VIC 3052 Australia > > E chris.adam...@mcri.edu.au > > www.mcri.edu.au > > > > > > This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, > confidential, may contain copyright material and is for the use only of the intended recipient. If > you receive the Communication in error, please notify the sender immediately by return e-mail, > delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal > with it. Any views expressed in the Communication are those of the individual sender only, unless > expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or > any of its related entities. MCRI does not accept liability in connection with the integrity of or > errors in the Communication, computer virus, data corruption, interference or delay arising from or > in respect of the Communication. > > > > P Please consider the environment before printing this email > > > > > This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mris_register problem
External Email - Use Caution Thanks Bruce. I had to increase the angular search range in the affine part to get it to work. Cheers, Chris. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Monday, 17 September 2018 11:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] mris_register problem Hi Chris you need to give us more information. What commands did you run? What was their output? Also, if you can send images of what you think is incorrect that might also be helpful cheers Bruce On Mon, 17 Sep 2018, Chris Adamson wrote: > > External Email - Use Caution > > Freesurfer experts, > > > > I'm having an issue with projecting labels from an atlas to a subject. I have > a static annot file on > the atlas that I want to paint onto my subject. The pipeline I have performed > is to mris_register my > subject to the atlas and then mri_surf2surf on the annot file using the > registered spherical > surfaces. > > > > The labels, when painted, are incorrectly oriented. How can I debug the > output of the registration > to check if the registration is working? I assume the registration works in > the 2D parameterised > space, can I extract parameterised versions of the curvature maps at each > iteration of the > registration. > > > > The strange thing is that when I view the spherical surfaces in freeview with > the overlaid curvature > maps they look in alignment prior to registration, but using this > unregistered sphere still puts the > labels in an incorrect orientation. So it appears as if there is some > rotation that is being done > internally that isn't shown in freeview. > > > > Please advise, > > > > Chris. > > > > Dr Chris Adamson > > Senior Research Officer > > Developmental Imaging, Clinical Sciences > > > > Murdoch Childrens Research Institute > > The Royal Children's Hospital > > Flemington Road, Parkville, VIC 3052 Australia > > E chris.adam...@mcri.edu.au<mailto:chris.adam...@mcri.edu.au> > > www.mcri.edu.au<http://www.mcri.edu.au> > > > > > > This e-mail and any attachments to it (the "Communication") are, unless > otherwise stated, > confidential, may contain copyright material and is for the use only of the > intended recipient. If > you receive the Communication in error, please notify the sender immediately > by return e-mail, > delete the Communication and the return e-mail, and do not read, copy, > retransmit or otherwise deal > with it. Any views expressed in the Communication are those of the individual > sender only, unless > expressly stated to be those of Murdoch Childrens Research Institute (MCRI) > ABN 21 006 566 972 or > any of its related entities. MCRI does not accept liability in connection > with the integrity of or > errors in the Communication, computer virus, data corruption, interference or > delay arising from or > in respect of the Communication. > > > > P Please consider the environment before printing this email > > > > > Disclaimer This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mris_register problem
Hi Chris you need to give us more information. What commands did you run? What was their output? Also, if you can send images of what you think is incorrect that might also be helpful cheers Bruce On Mon, 17 Sep 2018, Chris Adamson wrote: External Email - Use Caution Freesurfer experts, I’m having an issue with projecting labels from an atlas to a subject. I have a static annot file on the atlas that I want to paint onto my subject. The pipeline I have performed is to mris_register my subject to the atlas and then mri_surf2surf on the annot file using the registered spherical surfaces. The labels, when painted, are incorrectly oriented. How can I debug the output of the registration to check if the registration is working? I assume the registration works in the 2D parameterised space, can I extract parameterised versions of the curvature maps at each iteration of the registration. The strange thing is that when I view the spherical surfaces in freeview with the overlaid curvature maps they look in alignment prior to registration, but using this unregistered sphere still puts the labels in an incorrect orientation. So it appears as if there is some rotation that is being done internally that isn’t shown in freeview. Please advise, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adam...@mcri.edu.au www.mcri.edu.au This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mris_register problem: "No such file or directory"
Hi, I've had time to come back to this problem. It was not solved after recreating the sphere. And plus, it happens in 30% of my subjects (Approximately). I have opened the sphere and I can see no problem there (nor there is any kind of error message after opening it. Could you tell me what files are used in the "mris_register -curv" command (appart from the obvious lh.sphere and lh.average.curvature.filled.buckner40.tif) in order to check if there is any problem with them. The fact that the original error message is "No such file or directory" is intriguing. Cheers. 2015-08-02 18:57 GMT+01:00 Bruce Fischl : > try opening it in tksurfer and see if it complains > > On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: > > Hi, >> >> Thanks for the quick answer. >> >> There was no error message in the previous steps. >> >> I started it with : mris_sphere -seed 1234 ../surf/lh.inflated >> ../surf/lh.sphere >> >> Although if the seed is the same, I am guessing that any non-deterministic >> process would have the same output. >> >> Is there a a way to automatically know if there was a problem in the >> sphere >> creation? >> >> Cheers. >> >> >> 2015-08-02 16:27 GMT+01:00 Bruce Fischl : >> hmm, something seems to be wrong maybe the the ?h.sphere. Can >> you try recreating it >> cheers >> Bruce >> On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: >> >> Hi all, >> >> I received an error in one of the steps of >> recon-all. The error is "No such >> file or directory" at the end of one of the >> registration processes. >> >> The step was mris_register -curv. The command was: >> >> mris_register -curv ../surf/lh.sphere >> /average/lh.average.curvature.filled.buckner40.tif >> ../surf/lh.sphere.reg >> >> I already checked that ../surf/lh.sphere and >> /average/lh.average.curvature.filled.buckner40.tif >> exist (and are >> readable). I also checked that the output directorry >> (../surf/ ) has the >> proper permisons to write. >> >> The version of mris_register is "stable5". >> >> Finally, the complete output message is (Please, >> note that the parts with <> >> have been edited by me for privacy reasons: >> >> # >> #@# Surf Reg lh Sun Aug 2 00:52:59 BST 2015 >> /scripts >> >> mris_register -curv ../surf/lh.sphere >> /average/lh.average.curvature.filled.buckner40.tif >> ../surf/lh.sphere.reg >> >> using smoothwm curvature for final alignment >> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 >> nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 >> nicks Exp $ >> reading surface from ../surf/lh.sphere... >> reading template parameterization from >> /average/lh.average.curvature.filled.buckner40.tif... >> MRISregister() --- >> max_passes = 4 >> min_degrees = 0.50 >> max_degrees = 64.00 >> nangles = 8 >> tol=5.0e-01, sigma=0.0, host=., nav=1024, >> nbrs=1, l_extern=1.000, >> l_parea=0.200, l_nlarea=1.000, l_corr=1.000, >> l_dist=5.000 >> using quadratic fit line minimization >> complete_dist_mat 0 >> rms 0 >> smooth_averages 0 >> remove_neg 0 >> ico_order 0 >> which_surface 0 >> target_radius 0.00 >> nfields 0 >> scale 0.00 >> desired_rms_height -1.00 >> momentum 0.95 >> nbhd_size -10 >> max_nbrs 10 >> niterations 25 >> nsurfaces 0 >> SURFACES 3 >> flags 16 (10) >> use curv 16 >> no sulc 0 >> no rigid align 0 >> mris->nsize 1 >> mris->hemisphere 0 >> randomSeed 0 >> >> tol=5.0e-01, sigma=0.0, host=., nav=1024, >> nbrs=1, l_extern=1.000, >> l_parea=0.200, l_nlarea=1.000, l_corr=1.000, >> l_dist=5.000 >> using quadratic fit line minimization >> >> 1 Reading lh.sulc >> curvature mean = -0.000, std = 0.575 >> curvature mean = 0.028, std = 0.935 >> curvature mean = -0.002, std = 0.850 >> Starting MRISrigidBodyAlignGlobal() >> d=64.00 min @ (16.00, 32.00, -64.00) sse = >> 463438.8, tmin=0.7880 >> d=16.00 min @ (0.00, -4.00, 4.00) sse = 460445.8, >> tmin=2.3467 >> d=8.00 min @ (0.00, 0.00, -2.00) sse = 460199.6, >>
Re: [Freesurfer] mris_register problem: "No such file or directory"
try opening it in tksurfer and see if it complains On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: Hi, Thanks for the quick answer. There was no error message in the previous steps. I started it with : mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere Although if the seed is the same, I am guessing that any non-deterministic process would have the same output. Is there a a way to automatically know if there was a problem in the sphere creation? Cheers. 2015-08-02 16:27 GMT+01:00 Bruce Fischl : hmm, something seems to be wrong maybe the the ?h.sphere. Can you try recreating it cheers Bruce On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: Hi all, I received an error in one of the steps of recon-all. The error is "No such file or directory" at the end of one of the registration processes. The step was mris_register -curv. The command was: mris_register -curv ../surf/lh.sphere /average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg I already checked that ../surf/lh.sphere and /average/lh.average.curvature.filled.buckner40.tif exist (and are readable). I also checked that the output directorry (../surf/ ) has the proper permisons to write. The version of mris_register is "stable5". Finally, the complete output message is (Please, note that the parts with <> have been edited by me for privacy reasons: # #@# Surf Reg lh Sun Aug 2 00:52:59 BST 2015 /scripts mris_register -curv ../surf/lh.sphere /average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /average/lh.average.curvature.filled.buckner40.tif... MRISregister() --- max_passes = 4 min_degrees = 0.50 max_degrees = 64.00 nangles = 8 tol=5.0e-01, sigma=0.0, host=., nav=1024, nbrs=1, l_extern=1.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.00 nfields 0 scale 0.00 desired_rms_height -1.00 momentum 0.95 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=., nav=1024, nbrs=1, l_extern=1.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization 1 Reading lh.sulc curvature mean = -0.000, std = 0.575 curvature mean = 0.028, std = 0.935 curvature mean = -0.002, std = 0.850 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 32.00, -64.00) sse = 463438.8, tmin=0.7880 d=16.00 min @ (0.00, -4.00, 4.00) sse = 460445.8, tmin=2.3467 d=8.00 min @ (0.00, 0.00, -2.00) sse = 460199.6, tmin=3.1967 d=4.00 min @ (0.00, 0.00, 1.00) sse = 459864.8, tmin=4.0376 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 459815.2, tmin=4.8841 d=1.00 min @ (0.00, -0.25, 0.25) sse = 459808.6, tmin=5.7246 d=0.50 min @ (0.12, 0.38, -0.38) sse = 459786.2, tmin=6.5623 mrisComputeCorrelationTerm: delta is not finite at vno 0 MRISrigidBodyAlignGlobal() done 6.56 min No such file or directory Linux 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1398979 exited with ERRORS at Sun Aug 2 01:00:20 BST 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks in advance. ___
Re: [Freesurfer] mris_register problem: "No such file or directory"
Hi, Thanks for the quick answer. There was no error message in the previous steps. I started it with : mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere Although if the seed is the same, I am guessing that any non-deterministic process would have the same output. Is there a a way to automatically know if there was a problem in the sphere creation? Cheers. 2015-08-02 16:27 GMT+01:00 Bruce Fischl : > hmm, something seems to be wrong maybe the the ?h.sphere. Can you try > recreating it > cheers > Bruce > > On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: > > Hi all, >> >> I received an error in one of the steps of recon-all. The error is "No >> such >> file or directory" at the end of one of the registration processes. >> >> The step was mris_register -curv. The command was: >> >> mris_register -curv ../surf/lh.sphere >> /average/lh.average.curvature.filled.buckner40.tif >> ../surf/lh.sphere.reg >> >> I already checked that ../surf/lh.sphere and >> /average/lh.average.curvature.filled.buckner40.tif exist (and are >> readable). I also checked that the output directorry (../surf/ ) has the >> proper permisons to write. >> >> The version of mris_register is "stable5". >> >> Finally, the complete output message is (Please, note that the parts with >> <> >> have been edited by me for privacy reasons: >> >> # >> #@# Surf Reg lh Sun Aug 2 00:52:59 BST 2015 >> /scripts >> >> mris_register -curv ../surf/lh.sphere >> /average/lh.average.curvature.filled.buckner40.tif >> ../surf/lh.sphere.reg >> >> using smoothwm curvature for final alignment >> $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ >> reading surface from ../surf/lh.sphere... >> reading template parameterization from >> /average/lh.average.curvature.filled.buckner40.tif... >> MRISregister() --- >> max_passes = 4 >> min_degrees = 0.50 >> max_degrees = 64.00 >> nangles = 8 >> tol=5.0e-01, sigma=0.0, host=., nav=1024, nbrs=1, >> l_extern=1.000, >> l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 >> using quadratic fit line minimization >> complete_dist_mat 0 >> rms 0 >> smooth_averages 0 >> remove_neg 0 >> ico_order 0 >> which_surface 0 >> target_radius 0.00 >> nfields 0 >> scale 0.00 >> desired_rms_height -1.00 >> momentum 0.95 >> nbhd_size -10 >> max_nbrs 10 >> niterations 25 >> nsurfaces 0 >> SURFACES 3 >> flags 16 (10) >> use curv 16 >> no sulc 0 >> no rigid align 0 >> mris->nsize 1 >> mris->hemisphere 0 >> randomSeed 0 >> >> tol=5.0e-01, sigma=0.0, host=., nav=1024, nbrs=1, >> l_extern=1.000, >> l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 >> using quadratic fit line minimization >> >> 1 Reading lh.sulc >> curvature mean = -0.000, std = 0.575 >> curvature mean = 0.028, std = 0.935 >> curvature mean = -0.002, std = 0.850 >> Starting MRISrigidBodyAlignGlobal() >> d=64.00 min @ (16.00, 32.00, -64.00) sse = 463438.8, tmin=0.7880 >> d=16.00 min @ (0.00, -4.00, 4.00) sse = 460445.8, tmin=2.3467 >> d=8.00 min @ (0.00, 0.00, -2.00) sse = 460199.6, tmin=3.1967 >> d=4.00 min @ (0.00, 0.00, 1.00) sse = 459864.8, tmin=4.0376 >> d=2.00 min @ (-0.50, -0.50, 0.00) sse = 459815.2, tmin=4.8841 >> d=1.00 min @ (0.00, -0.25, 0.25) sse = 459808.6, tmin=5.7246 >> d=0.50 min @ (0.12, 0.38, -0.38) sse = 459786.2, tmin=6.5623 >> mrisComputeCorrelationTerm: delta is not finite at vno 0 >> MRISrigidBodyAlignGlobal() done 6.56 min >> No such file or directory >> Linux 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 >> x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s 1398979 exited with ERRORS at Sun Aug 2 01:00:20 BST 2015 >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> Thanks in advance. >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 n
Re: [Freesurfer] mris_register problem: "No such file or directory"
hmm, something seems to be wrong maybe the the ?h.sphere. Can you try recreating it cheers Bruce On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: Hi all, I received an error in one of the steps of recon-all. The error is "No such file or directory" at the end of one of the registration processes. The step was mris_register -curv. The command was: mris_register -curv ../surf/lh.sphere /average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg I already checked that ../surf/lh.sphere and /average/lh.average.curvature.filled.buckner40.tif exist (and are readable). I also checked that the output directorry (../surf/ ) has the proper permisons to write. The version of mris_register is "stable5". Finally, the complete output message is (Please, note that the parts with <> have been edited by me for privacy reasons: # #@# Surf Reg lh Sun Aug 2 00:52:59 BST 2015 /scripts mris_register -curv ../surf/lh.sphere /average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /average/lh.average.curvature.filled.buckner40.tif... MRISregister() --- max_passes = 4 min_degrees = 0.50 max_degrees = 64.00 nangles = 8 tol=5.0e-01, sigma=0.0, host=., nav=1024, nbrs=1, l_extern=1.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.00 nfields 0 scale 0.00 desired_rms_height -1.00 momentum 0.95 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=., nav=1024, nbrs=1, l_extern=1.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization 1 Reading lh.sulc curvature mean = -0.000, std = 0.575 curvature mean = 0.028, std = 0.935 curvature mean = -0.002, std = 0.850 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 32.00, -64.00) sse = 463438.8, tmin=0.7880 d=16.00 min @ (0.00, -4.00, 4.00) sse = 460445.8, tmin=2.3467 d=8.00 min @ (0.00, 0.00, -2.00) sse = 460199.6, tmin=3.1967 d=4.00 min @ (0.00, 0.00, 1.00) sse = 459864.8, tmin=4.0376 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 459815.2, tmin=4.8841 d=1.00 min @ (0.00, -0.25, 0.25) sse = 459808.6, tmin=5.7246 d=0.50 min @ (0.12, 0.38, -0.38) sse = 459786.2, tmin=6.5623 mrisComputeCorrelationTerm: delta is not finite at vno 0 MRISrigidBodyAlignGlobal() done 6.56 min No such file or directory Linux 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1398979 exited with ERRORS at Sun Aug 2 01:00:20 BST 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks in advance. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
