Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30096 discussions

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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cortical thickness in freesurfer
by anthony gallo 05 Apr '06

05 Apr '06

Hello, I am wondering how to view cortical thickness data in freesurfer. thanks

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Re: [Freesurfer] mri_watershed: dyld error on OS X 10.3.9
by Xander Meadow 05 Apr '06

05 Apr '06

Hi Nick, I tried running mri_watershed on Anthony's computer today and got a different error from last time. I got the following error: % freesurfer/bin/mri_watershed dyld: freesurfer/bin/mri_watershed can't open library: /usr/pubsw/packages/gsl/current/lib/libgsl.0.dylib (No such file or directory, errno = 2) Trace/BPT trap So I installed gsl and gsl-shlibs, and I've gotten mri_watershed to work for me. I will have Anthony and then another user try it out to see if installing gsl fixed the issue and let you know. Thank you. >Xander On Apr 4, 2006, at 4:05 PM, Nick Schmansky wrote: > Anthony, > > I don't know what to recommend. I cannot seem to find this symbol > defined anywhere (even Googling it). The panther distribution has > worked > for two other people (that i know of) outside of MGH, so I'm not sure > what I can suggest. The 'otool' output looks correct. > > If I can think of any other debugging techniques to try, I will send > them along. > > Nick > > > On Mon, 2006-04-03 at 14:06 -0500, Anthony Steven Dick wrote: >> Hi Nick-- >> >> I'm responding on behalf of Xander (our computer tech): >> >> [serge:NL-GCS/subjects/freesurfer_3.0.1] adick% otool -L `which >> mri_watershed` >> >> /Applications/freesurfer/bin//mri_watershed: >> >> /usr/pubsw/packages/gsl/current/lib/libgsl.0.dylib (compatibility >> version 8.0.0, current version 8.0.0) >> /usr/pubsw/packages/gsl/current/lib/libgslcblas.0.dylib (compatibility >> version 1.0.0, current version 1.0.0) >> /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version >> 1.2.3) >> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current >> version >> 88.1.5) >> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current >> version >> 7.3.0) >> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current >> version >> 1.0.0) >> /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version >> 92.0.0) >> >> Anthony >> >> >> Nick Schmansky wrote: >>> Can you send me the output of: >>> >>> otool -L `which mri_watershed` >>> >>> >>> >>> On Mon, 2006-04-03 at 13:34 -0500, xmeadow(a)uchicago.edu wrote: >>> >>>> Hi, >>>> >>>> I just downloaded and installed from: >>>> >>>> http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin- >>>> panther- >>>> stable-pub-v3.0.1-full.dmg >>>> >>>> And installed Freesurfer. Most of the apps have worked without a >>>> problem, >>>> however mri_watershed yields the following error: >>>> >>>> dyld: mri_watershed Undefined symbols: >>>> _acns >>>> Trace/BPT trap >>>> >>>> I have redowndloaded the above package and tried to extract >>>> mri_watershed, in >>>> case I just got a corrupted binary, but each time I do so I get the >>>> same errors. >>>> My machine is running MAC OS X 10.3.9. Please let me know if there >>>> is any fix I >>>> can do for this error? Thank you very much. >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >> >

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having problem in runing recon-all
by Shahabuddin Ansari 04 Apr '06

04 Apr '06

Hello, I am having a problem in running recon-all command. I have run this command without any problem. Today I moved the image into another directory and getting the following error: mri_convert /ensc/IMAGE4/STUDENTS/SANSARI/freesurfer/subjects/4365 /ensc/IMAGE/opt/FREESURFER/subjects/4365/mri/orig/001.mgz corRead(): can't open file /ensc/IMAGE4/STUDENTS/SANSARI/freesurfer/subjects/4365/COR-.info reading from /ensc/IMAGE4/STUDENTS/SANSARI/freesurfer/subjects/4365... Linux ilpc5 2.4.20-30.9smp #1 SMP Wed Feb 4 20:36:46 EST 2004 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Tue Apr 4 13:10:59 PDT 2006 Thanks Shahab __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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mri_watershed: dyld error on OS X 10.3.9
by xmeadow＠uchicago.edu 03 Apr '06

03 Apr '06

Hi, I just downloaded and installed from: http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Darwin-panther- stable-pub-v3.0.1-full.dmg And installed Freesurfer. Most of the apps have worked without a problem, however mri_watershed yields the following error: dyld: mri_watershed Undefined symbols: _acns Trace/BPT trap I have redowndloaded the above package and tried to extract mri_watershed, in case I just got a corrupted binary, but each time I do so I get the same errors. My machine is running MAC OS X 10.3.9. Please let me know if there is any fix I can do for this error? Thank you very much.

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