Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

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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64 vs 32
by Sasha Wolosin 17 Nov '05

17 Nov '05

Dear all, I have run several subjects on a 64-bit machine using the stable release. I recently installed the 32-bit stable version on a 32-bit machine. I noticed that running stage1 on the 32-bit version took much longer than running stage1 on the 64-bit machine (several hours, actually). So I looked at the recon-all scripts for each version and I noticed that they were different. The 32-bit version includes the extra steps DoGCAReg, DoCANormalize, DoCAReg, and DoCALabel. Does anyone know why this is? Below are the stage1 lists for each version. Thanks, Sasha 32-bit version: case "-stage1": set DoMotionCor = 1; set DoTalairach = 1; set DoNuIntensityCor = 1; set DoNormalization = 1; set DoSkullStrip = 1; set DoSegmentation = 1; set DoGCAReg = 1; set DoCANormalize = 1; set DoCAReg = 1; set DoCALabel = 1; set DoFill = 1; set DoTessellate = 1; set SvInitOrigSurf = 1; set DoSmooth1 = 1; set DoInflate1 = 1; set SvInitInflated = 1; breaksw 64-bit version: case "-stage1": set DoMotionCor = 1; set DoTalairach = 1; set DoNuIntensityCor = 1; set DoNormalization = 1; set DoSkullStrip = 1; set DoSegmentation = 1; set DoFill = 1; set DoTessellate = 1; set SvInitOrigSurf = 1; set DoSmooth1 = 1; set DoInflate1 = 1; set SvInitInflated = 1; breaksw 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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Re: mris_ca_label 32vs64 (Satrajit Ghosh)
by Sasha Wolosin 17 Nov '05

17 Nov '05

Dear all, I have also noticed a discrepancy between the stable 32 and the stable 64. The FreeSurferEnv.csh files are quite different. Why is that? Are there any other differences? 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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mris_ca_label 32vs64
by Satrajit Ghosh 17 Nov '05

17 Nov '05

I'm noticing some discrepancies between the 64 bit and the 32 bit version of mris_ca_label. I've shown the output from the 64 bit version and the 32 bit version operating on the same subject. I'm using are the dev versions for centos from the download site. To note: 1. In the 64 bit version I get the following output during the process: GCSANclassify: could not find GCS for node 0! Numerical result out of range The 32 bit version does not generate this error on either on th 64 bit machine or a 32 bit machine. 2. The numerical values listed for changed and examined are different. This could well be the case if there was some random element being used. Thanks, Satra ******************** 64 bit output *********************** [satra@sweetsixteen subjects]$ FSParc/roi_classify cape01.02 reading atlas from /speechlab/software/freesurfer.64/subjects/average/lh.SpeechLabAtlas02.gcs.. . input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 12146 changed, 161370 examined... 001: 2766 changed, 44430 examined... 002: 867 changed, 13696 examined... 003: 356 changed, 4560 examined... 004: 174 changed, 2006 examined... 005: 99 changed, 984 examined... 006: 56 changed, 525 examined... 007: 35 changed, 299 examined... 008: 20 changed, 197 examined... 009: 13 changed, 110 examined... 010: 4 changed, 90 examined... 011: 4 changed, 22 examined... 012: 0 changed, 11 examined... 000: 296 total segments, 236 labels (2598 vertices) changed 001: 76 total segments, 16 labels (103 vertices) changed 002: 60 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 95 changed) writing output to lh-aparc.annot... classification took 1 minutes and 29 seconds. reading atlas from /speechlab/software/freesurfer.64/subjects/average/rh.SpeechLabAtlas02.gcs.. . input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... GCSANclassify: could not find GCS for node 0! Numerical result out of range GCSANclassify: could not find GCS for node 0! Numerical result out of range GCSANclassify: could not find GCS for node 0! Numerical result out of range relabeling using gibbs priors... 000: 10608 changed, 158433 examined... 001: 2326 changed, 38991 examined... 002: 725 changed, 11759 examined... 003: 307 changed, 3966 examined... 004: 150 changed, 1744 examined... 005: 51 changed, 827 examined... 006: 26 changed, 287 examined... 007: 12 changed, 146 examined... 008: 11 changed, 79 examined... 009: 11 changed, 54 examined... 010: 7 changed, 56 examined... 011: 6 changed, 38 examined... 012: 4 changed, 30 examined... 013: 2 changed, 21 examined... 014: 5 changed, 10 examined... 015: 0 changed, 17 examined... 000: 233 total segments, 174 labels (2403 vertices) changed 001: 72 total segments, 14 labels (54 vertices) changed 002: 58 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 91 changed) writing output to rh-aparc.annot... classification took 1 minutes and 21 seconds. *********************** 32 bit output on 64 bit machine ******** [satra@sweetsixteen subjects]$ FSParc/roi_classify cape01.02 reading atlas from /speechlab/software/freesurfer.32/subjects/average/lh.SpeechLabAtlas02.gcs.. . input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 12079 changed, 161370 examined... 001: 2690 changed, 44278 examined... 002: 810 changed, 13380 examined... 003: 361 changed, 4352 examined... 004: 178 changed, 2025 examined... 005: 105 changed, 1038 examined... 006: 69 changed, 608 examined... 007: 44 changed, 381 examined... 008: 26 changed, 233 examined... 009: 18 changed, 162 examined... 010: 7 changed, 106 examined... 011: 3 changed, 48 examined... 012: 2 changed, 21 examined... 013: 1 changed, 12 examined... 014: 0 changed, 5 examined... 000: 293 total segments, 234 labels (2674 vertices) changed 001: 78 total segments, 19 labels (100 vertices) changed 002: 59 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 86 changed) writing output to lh-aparc.annot... classification took 1 minutes and 52 seconds. reading atlas from /speechlab/software/freesurfer.32/subjects/average/rh.SpeechLabAtlas02.gcs.. . input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 10576 changed, 158433 examined... 001: 2384 changed, 38916 examined... 002: 683 changed, 11993 examined... 003: 313 changed, 3870 examined... 004: 164 changed, 1744 examined... 005: 94 changed, 929 examined... 006: 49 changed, 502 examined... 007: 20 changed, 286 examined... 008: 13 changed, 114 examined... 009: 7 changed, 75 examined... 010: 5 changed, 44 examined... 011: 4 changed, 27 examined... 012: 3 changed, 20 examined... 013: 4 changed, 19 examined... 014: 2 changed, 20 examined... 015: 3 changed, 14 examined... 016: 3 changed, 20 examined... 017: 1 changed, 16 examined... 018: 0 changed, 7 examined... 000: 230 total segments, 173 labels (2273 vertices) changed 001: 66 total segments, 9 labels (28 vertices) changed 002: 57 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 83 changed) writing output to rh-aparc.annot... classification took 1 minutes and 42 seconds. *********************** 32 bit output on 32 bit machine ******************* [satra@four subjects]$ FSParc/roi_classify cape01.02 reading atlas from /speechlab/software/freesurfer.32/subjects/average/lh.SpeechLabAtlas02.gcs.. . input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 12040 changed, 161370 examined... 001: 2723 changed, 44275 examined... 002: 794 changed, 13548 examined... 003: 348 changed, 4370 examined... 004: 185 changed, 1950 examined... 005: 101 changed, 1035 examined... 006: 76 changed, 607 examined... 007: 39 changed, 422 examined... 008: 25 changed, 223 examined... 009: 13 changed, 126 examined... 010: 5 changed, 65 examined... 011: 3 changed, 27 examined... 012: 4 changed, 20 examined... 013: 1 changed, 22 examined... 014: 2 changed, 5 examined... 015: 2 changed, 11 examined... 016: 2 changed, 10 examined... 017: 1 changed, 9 examined... 018: 0 changed, 9 examined... 000: 288 total segments, 226 labels (2311 vertices) changed 001: 79 total segments, 17 labels (109 vertices) changed 002: 62 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 104 changed) writing output to lh-aparc.annot... classification took 3 minutes and 8 seconds. reading atlas from /speechlab/software/freesurfer.32/subjects/average/rh.SpeechLabAtlas02.gcs.. . input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 10629 changed, 158433 examined... 001: 2376 changed, 39027 examined... 002: 729 changed, 12097 examined... 003: 325 changed, 4004 examined... 004: 183 changed, 1848 examined... 005: 91 changed, 982 examined... 006: 51 changed, 512 examined... 007: 38 changed, 284 examined... 008: 22 changed, 205 examined... 009: 12 changed, 133 examined... 010: 3 changed, 74 examined... 011: 3 changed, 16 examined... 012: 2 changed, 16 examined... 013: 2 changed, 10 examined... 014: 2 changed, 12 examined... 015: 2 changed, 10 examined... 016: 2 changed, 10 examined... 017: 3 changed, 12 examined... 018: 1 changed, 16 examined... 019: 0 changed, 7 examined... 000: 230 total segments, 173 labels (2426 vertices) changed 001: 65 total segments, 9 labels (61 vertices) changed 002: 56 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 83 changed) writing output to rh-aparc.annot... classification took 3 minutes and 5 seconds.

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atlas and coordinate
by Antao Du 16 Nov '05

16 Nov '05

Hi, I processed a bunch of data using the version of 2004 freesurfer. what is the atlas and the coordinate file for each locations used in mris_anatomical_stats? Thanks, Antao

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tkmedit
by Sasha Wolosin 16 Nov '05

16 Nov '05

Dear all, My brains appear too bright after skull stripping, so I tried to fix this with the following command: tkmedit 2316_corffe brain -mm-main 0 255 But the --mm-main option did not have an effect unless I set the max to be lower than the actual max (which was about 170 in this case) The brightness/contrast gui in the tkmedit menu does not allow me to increase the max either. I am using the stable release for x86_64 machines. 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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