Hi, there,
recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions?
gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed.
not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010
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What version are you running?
On Mar 13, 2010, at 4:22 PM, Guang Zeng freesurfer_zg@hotmail.com wrote:
Hi, there,
recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions?
gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed.
not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010
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I use v4.5.0, I also downloaded the new version of mri_label and tried it, but I got another error says that
" mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /home/m047599/freesurfer-install/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz /home/m047599/freesurfer-install/freesurfer/bin/mri_ca_label: Permission denied."
Thanks! Guang
From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com Date: Sat, 13 Mar 2010 17:03:05 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all fails because of mri_label error
What version are you running?
On Mar 13, 2010, at 4:22 PM, Guang Zeng freesurfer_zg@hotmail.com wrote:
Hi, there,
recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions?
gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed.
not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010
The New Busy is not the old busy. Search, chat and e-mail from your inbox. Get started. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:W...
Hello, Bruce,
I loaded the brainmask.mgz, it has a bad skull-stripping results with cerebellum attached. I tried to fix this problem by adjusting the watershed parameters, but the interesting thing is:
this is the base template subject which is created by the command line recon-all -base base_id -tp subj1 -tp subj2 -all
I am not sure what is next command line I need to use after I fix the skull-stripping problem,
recon-all -base base_id -tp subj1 -tp subj2 -autorecon2 or recon-all -s base_id -autorecon2
Thanks! Guang
From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com Date: Sat, 13 Mar 2010 17:03:05 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all fails because of mri_label error
What version are you running?
On Mar 13, 2010, at 4:22 PM, Guang Zeng freesurfer_zg@hotmail.com wrote:
Hi, there,
recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions?
gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed.
not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010
The New Busy is not the old busy. Search, chat and e-mail from your inbox. Get started. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/210850552/direct/01/
Hi Guang,
yes, this should work: recon-all -base base_id -tp subj1 -tp subj2 -autorecon2 -autorecon3
Let us know how it goes,
-Martin
On Mon, 2010-03-15 at 10:31 -0500, Guang Zeng wrote:
Hello, Bruce,
I loaded the brainmask.mgz, it has a bad skull-stripping results with cerebellum attached. I tried to fix this problem by adjusting the watershed parameters, but the interesting thing is:
this is the base template subject which is created by the command line recon-all -base base_id -tp subj1 -tp subj2 -all
I am not sure what is next command line I need to use after I fix the skull-stripping problem,
recon-all -base base_id -tp subj1 -tp subj2 -autorecon2 or recon-all -s base_id -autorecon2
Thanks! Guang
From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com Date: Sat, 13 Mar 2010 17:03:05 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all fails because of mri_label error
What version are you running?
On Mar 13, 2010, at 4:22 PM, Guang Zeng freesurfer_zg@hotmail.com wrote:
Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010 ______________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. Get started. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Guang Zeng -
Martin Reuter