Freesurfer November 2005

freesurfer@nmr.mgh.harvard.edu

49 participants
73 discussions

Normalization problem
by Martin Ystad 21 Nov '05

21 Nov '05

I'm working on the latest developmental release for Rh. 9. and I'm having problems with the normalization procedures on my datasets. My datasets have large intensity inhomogeneities due to their acquisition with a surface coil (8-ch. GE). To fix this problem I have resorted to the use of control points. This works if I add enough points across the brain ( over 200), and I get a better normalization result after running "recon-all -normalization -usecontrolpoints" and another skull-stripping on the new T1-volume. To test whether or not this produces a good segmentaition of white matter, I run mri_segment on my brain.mgz -volume. If I'm satisfied with the segmentation result, I move on to the surface processing stage, and run the -autorecon2 -script. The problem is that after running the -autorecon2, the normalization is completely wrong again, looking more like the first normalization done without control points, and the wm.mgz -volume is also bad. So are the surfaces. How do I make freesurfer produce the same good results as I got during the first normalization? Do I need to specify the use of control points again, even though the brain.mgz volume looks ok? Thanks, Martin Ystad Medical Student University of Bergen Institute of Biomedicine Jonas Lies vei 91, 5009 Bergen, Norway.

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warning
by Sasha Wolosin 21 Nov '05

21 Nov '05

Dear all, I see this warning for several different commands, does anyone know what this means? INFO: Volume /tmp/mritotal_32685/nu_8_dxyz.mnc cannot be found. Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Freesurfer mailing list and google
by Satrajit Ghosh 21 Nov '05

21 Nov '05

Dear freesurfer users, By adding the following phrase to google's search box, you can search the freesurfer mailing list archives. site:https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ I have found this extremely useful. Satra

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Normalization problem
by Martin Ystad 20 Nov '05

20 Nov '05

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problems with process volume
by hengameh haghighat 18 Nov '05

18 Nov '05

Hello I have three problems with FreeSurfer software. 1- I don't know how to segment the hippocampus with FreeSurfer software. For this reason i segmentated the hippocampus with another software (MRIcro) and then gave these slides to FreeSurfer software for measuring volume of hippocampus. The obtained volume was greater than the normal volume. For this reason I made a phantom with the specific volume of 27.142 cm3 to obtained correction factor. 2- In the guide's FreeSurfer it is said when watershed algorithm is corrupted , change the preflooding height to 30% in the setting section of RmSkull tab in expert preference , however I didn't get any result. 3- when an analyze file including one slide or all of the taken slides are given to the FreeSurfer software the watershed algorithm is corrupted and the volume is not calculated . 4- How much is the difference between the volume of the subject brain with FreeSurfer software (Albert) and the obtained volume in FreeSurfer software? how have you obtained it's correction factor? I would be thankful if you help me in this matter. I look forward to hearing for you soon Sincerely Yours -- Tehran University of Medical Sciences (www.tums.ac.ir)

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request for guide (fwd)
by Xiao Han 18 Nov '05

18 Nov '05

I am forwarding Hengameh's questions to the list since I am not sure about the answers and somehow she couldn't send emails to the list (do people need to subscribe to the list first?). Please help if you know the answers to her questions. Thanks, -Xiao ---------------------------------------- From: hengameh haghighat <hhaghighat(a)razi.tums.ac.ir> I have three problems with FreeSurfer software. 1- I don't know how to segment the hippocampus with FreeSurfer software. For this reason i segmentated the hippocampus with another software (MRIcro) and then gave these slides to FreeSurfer software for measuring volume of hippocampus. The obtained volume was greater than the normal volume. For this reason I made a phantom with the specific volume of 27.142 cm3 to obtained correction factor. 2- In the guide's FreeSurfer it is said when watershed algorithm is corrupted , change the preflooding height to 30% in the setting section of RmSkull tab in expert preference , however I didn't get any result. 3- when an analyze file including one slide or all of the taken slides are given to the FreeSurfer software the watershed algorithm is corrupted and the volume is not calculated . 4- How much is the difference between the volume of the subject brain with FreeSurfer software (Albert) and the obtained volume in FreeSurfer software? how have you obtained it's correction factor? I would be thankful if you help me in this matter. I look forward to hearing for you soon Sincerely Yours

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libs?
by Antao Du 18 Nov '05

18 Nov '05

Hi, I installed freesurfer in a new machine (Fedora 4) and when I run -skullstrip, an error message appeared as the following. It seems a error from a library libstdc++.so.5. In this machine, libstdc++.so.6 exists. Can someone tell me how to fix the problem Thanks, Antao [antao@localhost subjects]$ recon-all -skullstrip -s FT035-1-1/ INFO: SUBJECTS_DIR is /home/antao/freesurfer/subjects Actual FREESURFER_HOME /home/antao/freesurfer Linux localhost.localdomain 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux ######################################## program versions used $Id: recon-all-nmr,v 1.114 2005/09/28 21:38:23 nicks Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ minctracc.c $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2005-08-31 at 17:44:16 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mri_normalize.c,v 1.37 2005/10/03 01:15:35 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 mri_watershed: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mri_fill.c,v 1.96 2005/09/20 21:22:12 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mris_fix_topology.c,v 1.32 2005/09/12 18:07:35 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mris_make_surfaces.c,v 1.60 2005/08/22 17:47:27 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mris_register.c,v 1.30 2005/08/15 14:24:44 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mri_label2label.c,v 1.21 2004/11/16 00:35:37 greve Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mri_em_register.c,v 1.50 2005/05/30 20:36:05 xhan Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mri_ca_register.c,v 1.35 2005/09/26 21:34:29 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 05/11/18-11:16:48-GMT CVS: $Id: mri_ca_label.c,v 1.62 2005/08/18 13:29:41 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.11-1.1369_FC4smp CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB40_talairach_2005-07-20.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### ~/freesurfer/subjects/FT035-1-1 Using mgz format --------------------------------------------- Skull Stripping Fri Nov 18 03:16:49 PST 2005 /home/antao/freesurfer/subjects/FT035-1-1/mri mri_watershed T1.mgz brain.mgz mri_watershed: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory ERROR: mri_watershed exited with non-zero status Linux localhost.localdomain 2.6.11-1.1369_FC4smp #1 SMP Thu Jun 2 23:08:39 EDT 2005 i686 i686 i386 GNU/Linux recon-all exited with errors at Fri Nov 18 03:16:49 PST 2005 [antao@localhost subjects]$ [antao@localhost subjects]$

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trouble with seq.info, solved
by Sebastian Moeller 18 Nov '05

18 Nov '05

Hi All, I just squashed a most embarrassing error in my sequence naming. The open encoding of the used TR in the protokollname (i.e. mak_epi_TR4) classed with the cheking code in mkanalysis-sess.new. There the grep for "TR" returned not only the TR line out of the seq.info file, but also the erroneously named sequence/protocol name, so 4 instead of 2. My quick and dirty fix was to make the grep find "TR " instead of "TR", as the sequence/protocol name is forbidden to contain whitespaces anyway. I am the first to admit the ugliness of this approach, but it solves the problem without having to rename the sequence. And unpacksdcmdir writes several spaces between the TR and the actual value into the seq.info file in the first place. Maybe relaying on those white spaces in the seq.info file could be used to relax the allowed components of the protocol name for all variables? Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Tksurfer tcl script LoadCurvature
by Henry Luetcke 18 Nov '05

18 Nov '05

Hi, is there a tcl-script command for loading a curvature file in tksurfer? If yes, what is it and what is the syntax? Actually, is there a reference document with all the script commands for tksurfer? Thank you very much in advance! Henry

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Re: [Freesurfer] 64 vs 32
by Sasha Wolosin 17 Nov '05

17 Nov '05

So why aren't they included in the 64-bit stable? How long would you expect these steps to take? Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Freesurfer November 2005