Re: [Freesurfer] retinotopy and FsFast
you should be running everything fromt the study dir. Often, your study dir is also the parent to the sessions. When it is not, then you need to supply a -d sesspar or -df sessparfile doug Jane Aspell wrote: Ok, thanks. It seems that the problem with finding the session came about because I was running 'sfa-sess' from the 'MYSTUDY' study directory when it seems i should have run it from the 'session parent' directory. cheers, Jane In message [EMAIL PROTECTED] Doug Greve [EMAIL PROTECTED] writes: that's a bug in the wiki, "-s avdk" should not appear there. Rather, it should be "-s yoursession" or "-sf sessidfile". If it cannot find the sessions, then something is not set up correctly. Can you double check that the sessions in the sessidfile are in the current directory? Jane Aspell wrote: Hi Thanks for all your previous help with freesurfer. I am trying to use FsFast to do retinotopy analysis and have been following the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis I come undone at the stage of running the actual analysis, where the command should be: sfa-sess -s avdk -a rtopy what does 'avdk' refer to? when i run it i get: ERROR: could not find session avdk when i try it with the arguments: sfa-sess -analysis rtopy -sf sessid which is similar to the arguments needed for 'selxavg-sess' i get a similar error of not been able to find my (particular subject's) session. i believe i have set up the all the directory structures etc correctly for the sessions format as previous steps worked fine. any ideas what's going wrong? thanks Jane Aspell ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Tksurfer tcl script LoadCurvature
On Thu, Nov 17, 2005 at 03:51:01PM +0100, Henry Luetcke wrote: is there a tcl-script command for loading a curvature file in tksurfer? It depends what version you're using, but if it's relatively recent: set curv FILE_NAME read_binary_curv; If yes, what is it and what is the syntax? Actually, is there a reference document with all the script commands for tksurfer? Sorry, not really. But if you have something you want to try and do, let me know and I'll give you the commands for it. -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] libs?
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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] (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
Re: [Freesurfer] libs?
Antao, Which platform release of Freesurfer did you install? The dev rh9 release or the dev centos4 release? I think for the Fedora 4 platform, you will want the dev centos4 release, which uses the libstdc++.so.6 libs. Nick 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] (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:
[Freesurfer] request for guide (fwd)
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 [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] request for guide (fwd)
yes, they need to subscribe at the surfer.nmr.mgh.harvard.edu website On Fri, 18 Nov 2005, Xiao Han wrote: 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 [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problems with process volume
Hi Hengameh, sorry, I don't understand most of these questions. We don't have an official release of the hippocampal segmentation software yet, although our development version can be downloaded, which contains the subcortical (including hippocampus) segmentation. What do you mean by slide? Do you mean slice? If so, you must give watershed all slices otherwise it won't work at all. And I don't understand 4 - which two volumes do you mean? cheers, Bruce On Fri, 18 Nov 2005, hengameh haghighat wrote: 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) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
