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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working file system and mri_convert of the sample data
by Nam, Euicheol 03 Apr '06

03 Apr '06

Hi, I am practicing freesurfer with the sample data downloaded from freesurfer wiki homepage. I have two questions. 1) My computer doesn't have enough memory capacity, so I saved the data on my USB memory, but I couldn't find how to make freesurfer work with the data in the USB memory drive. Is it possible? According to the tutorial, I have to move the data to FREESUFER_HOME directory of my laptop Linux system. 2) Thus, I moved the sample data to FREESURFER_HOME directory in my computer hard drive but I found another problem in doing mri_convert data. The given sample data was, " buckner_data-tutorial_subjs" I made directory as "mksubjdirs anon" then, cd $FREESURFER_HOME/subjects/buckner_data/tutorial_subjs and setenv {SUBJECTS_DIR} ${PWD} But when I tried to convert files as the tutorial said mri_convert 014-anon/001.dcm ${SUBJECTS_DIR}/anon/mri/orig/001.mgz this command could not be executed and the error message came up "014-anon/001.dcm file or directory does not exist". I guess "anon" directory couldn't have any dcm files because I made the directory in FREESURFER_HOME. And actually I couldn't find any dcm files in the sample data. I'll appreciate if I can get help from you.

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RE: [Freesurfer] how to register subcortical segmentation with theoriginal image
by Durastanti, Valentina (NIH/NINDS) [F] 01 Apr '06

01 Apr '06

Hi, I'm trying to run -autorcon1 of a subject who has 3 mgz images but always came out an error about the motion correction. So I tried run the step using just 1 image and it has gone fine! Have you any suggestion about the reason? The images look good! Thanks Valentina

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Outputting reformatted images in freesurfer
by Salil Soman 01 Apr '06

01 Apr '06

Hi, I have 2 images loaded into freesurfer (1 as an overlay) with the images transformed using a .reg file. Is there a way in freesurfer to output each of the loaded images in the pose they are in after loading the .reg file? (so the pose of each image is the result of whatever transforms are applied to the images by the .reg file) The end result I'm looking for is that is both images are loaded into freesurfer with a reg file that applies no transforms, the images will be the same as though the original .reg file was used. Thanks, Salil Soman sal(a)bwh.harvard.edu

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new to Freesurfer
by Chacko Cherian 01 Apr '06

01 Apr '06

Hello there, I am a Graduate research assistant at a Neuroimage analysis lab.I am starting to use Freesurfer for image analysis at our labs.Could you please let me know about any prerequisites which I would need before starting to use this tool.(I presume Tcl would be gud to know).Your advice will help me a long way in my work Thanks in advance Take care Chacko Cherian. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Problem
by Tracy Abildskov 01 Apr '06

01 Apr '06

Hello, I just installed FreeSurfer following the instructions that were outlined on the web site. Now I am testing the installation also following the instructions on the web site. The following is the error that I got. [psyched@byu321453wks freesurfer]$ pwd /usr/local/freesurfer [psyched@byu321453wks freesurfer]$ tkmedit bert orig.mgz tkmedit: error while loading shared libraries: libtix.so.0: cannot open shared object file: No such file or directory [psyched@byu321453wks freesurfer]$ Are there other packages that I need to install to get freesurfer to run? Thanks, Tracy

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RE: [Freesurfer] lh.curv versus lh.curv.pial
by Durastanti, Valentina (NIH/NINDS) [F] 30 Mar '06

30 Mar '06

thanks Valentina -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, March 30, 2006 12:44 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] lh.curv versus lh.curv.pial depends on what kind of machine, but yes it can take that long (sorry) Bruce On Thu, 30 Mar 2006, Durastanti, Valentina (NIH/NINDS) [F] wrote: > > > Hi, > I've a question: I'm running the autorecon2 of some subjects and I > realized that they take more than 24 hours to finish it. Is it possible? > I know that the step can take upwards of 15 hours but I was wondering if > it is too much! > > Thanks > > Valentina > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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