Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30060 discussions

tcl command to raise tksurfer window
by Darren Weber 07 Apr '06

07 Apr '06

Hi Kevin, how do we raise the tksurfer window into the foreground in a tcl script (in case it is obscured by other windows)? Best, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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tcl help with labl_set_color
by Darren Weber 06 Apr '06

06 Apr '06

Hi, I'm a novice with tcl, so I'm having trouble with using a variable to labl_set_color index r g b eg, set color "255 255 255" labl_set_color 0 $color gives error: Wrong # args: labl_set_color index r g b How is this done? Thanks, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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tcl command to change tksurfer background
by Darren Weber 06 Apr '06

06 Apr '06

Hi Kevin, is there a tcl command to set the tksurfer background to white? Thanks, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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recon-all problem: skull stripping asks for COR-.info files that do not exist
by Nguyen, Thang Q 06 Apr '06

06 Apr '06

Hello all, I'm not sure if this is a problem with the incorporation of the mgz format or not but when I run recon-all, the skull stripping step requests for COR-.info files. The only format that I have in the mri folder is the mgz format. Is there an override option that tells recon-all that I am using mgz format that I don't see? Thank you for your help, Thang Nguyen

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FW: recon-all problem: skull stripping asks for COR-.info files that do not exist
by Nguyen, Thang Q 06 Apr '06

06 Apr '06

Forgot to include the message: Skull Stripping Thu Apr 6 10:09:25 PDT 2006 /subject12/mri mri_mask -xform /subject1/mri/transforms/Subject1_to_Subject12.lta T1 /subject1/mri/brain brain transform file name is /subject1/mri/transforms/Subject1_to_Subject12.lta corRead(): can't open file /subject1/mri/brain/COR-.info mri_mask: could not read mask volume T1 --------------------------------------------- Segmentation Thu Apr 6 10:09:28 PDT 2006 ERROR: cannot find brain/COR-.info recon-all exited with errors at Thu Apr 6 10:09:28 PDT 2006 -----Original Message----- From: Nguyen, Thang Q Sent: Thursday, April 06, 2006 10:27 AM To: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: recon-all problem: skull stripping asks for COR-.info files that do not exist Hello all, I'm not sure if this is a problem with the incorporation of the mgz format or not but when I run recon-all, the skull stripping step requests for COR-.info files. The only format that I have in the mri folder is the mgz format. Is there an override option that tells recon-all that I am using mgz format that I don't see? Thank you for your help, Thang Nguyen

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recon-all -subjid < > -autorecon2
by anthony gallo 06 Apr '06

06 Apr '06

I have tried to run this command 2 times and it does not seem to finish the command. The log file just says: Em registration (date/time) CA Normalization (date/time) CA Reg (date/time) The log file ends each time with Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4319 voxels, overlap= 0.599) aligning Right_Thalamus_Proper... source mean =83.5658, std = 26.5322 X:99-132; Y:128-155; Z:103-141 gca peak = 0.06253 (102\n\n then that is it. No formal error presents but there is nonprogression. Any ideas? Thanks (again...and again)

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tksurfer - cuvature - thickness
by anthony gallo 06 Apr '06

06 Apr '06

I loaded the curvature -> thickness file.......I don't understand how this gives you thickness measurments. On the surfer interface what are the distance and curvature numbers measured in.....what are the units? What is taken as center for those measurements as well? Thanks very much for your help!

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tksurfer script and window resize
by Darren Weber 05 Apr '06

05 Apr '06

Hi Kevin, tksurfer is great, but I need your advice about something bugging me --- maybe you experience it also. I am trying to run a script that flips views and saves out tiff files. I want to do this with a large window, so I have the following near the start of the tcl script: move_window 0 0 resize_window 1000 redraw update UpdateAndRedraw Whenever I call this script for tksurfer, whether using the -tcl option or through tools->Run Script or by source at the tcl command prompt, it runs all the commands in the script after these commands before actually updating the screen position and size. This is despite the 'update' commands. This means that when the commands to rotate the view and save out graphics are actually executed, the window is not the right size. This a real puzzle that bugs me and I can't debug it. I don't fully understand the process model at work here. I can't tell whether this is a tcl, opengl, gnome or kernel scheduling issue (but I think it works in that order). Is this common to all systems or have I got a quirk? I'm running Debian stable (mostly), with nvidia kernel module in a 2.6.8 kernel. Best, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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Nu_correct error
by Frederick Powell 05 Apr '06

05 Apr '06

Hello I am a Grad student with Dr. Killiany at Boston University. I am running auto recon with a Linux Centos machine. So I am running the auto recon on his system while controlling from my mac machine. I recieved the following error. I am not Linux savy so will need some detailed help. Thanks nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct -- Frederick G. Powell Boston University School of Medicine MD/PhD candidate 617-593-7183

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RE: [Freesurfer] cortical thickness in freesurfer
by Kirk, Gregory 05 Apr '06

05 Apr '06

While on the subject of cortical thickness. Looking at the new tutorial there is an expanded section on cluster analysis. If my reading is correct the best way to get P values for a study is to do the cluster analysis on the group analysis results and use the P value bounds obtained As a result to publish, etc. This would be a corrected P value if the simulation correction Is used ? Thanks Greg. -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Wednesday, April 05, 2006 12:08 PM To: anthony gallo Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cortical thickness in freesurfer tksurfer -> file -> load curvature -> ?h.thickness On Wed, 5 Apr 2006, anthony gallo wrote: > Hello, I am wondering how to view cortical thickness data in > freesurfer. thanks > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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