Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30078 discussions

freesurfer release v4.0.1
by Nick Schmansky 18 Sep '07

18 Sep '07

Freesurfer stable release v4.0.1 is now available. This is a bug-fix release, described on the Release Notes page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes

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re-run FreeSurfer with v4
by Xiangchuan Chen 17 Sep '07

17 Sep '07

Hi all, I am working on 80 subjects' data with the following work flow: 1. -autorecon1 2. edit talairach registration 3. -autorecon1 4. -autorecon2 5. edit brainmask.mgz 6. edit wm.mgz 7. -autorecon2-wm 8. -autorecon3 I have already finished this work flow for 30 subjects with FreeSurfer v3.05. I have spent a lot of time on steps 2, 5 and 6. I am not worrying about the other steps because they are my computer's tasks, but not mine. So, if I re-run the same work flow with v4, do I have to go through all these steps? Any suggestions are greatly appreciated. Thanks in advance, Xiangchuan Chen

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Re: Re: [Freesurfer] centos4_x86_64_V4.0 vs. centos4_V4.0
by Xiangchuan Chen 17 Sep '07

17 Sep '07

Hi Nick, Thank you for replying to my questions. I am glad to know why the centos4_x86_64_v4.0 version did not work on my laptop. For the tkmedit issue, the + and - icons next to the slice number entry box, and the arrow keys all work very well when I want to change the slice number one by one. But, I am not able to enter numbers into the slice number box. It may be inconvenient if I want to jump from slice #128 to slice #35. Thanks, Xiangchuan ======== Start Of Original Message ======== Date: 2007-09-17 Time: 13:50:28 From: Nick Schmansky (nicks(a)nmr.mgh.harvard.edu) To: Xiangchuan Chen (xiangchuan.chen(a)bme.emory.edu) Subject: Re: [Freesurfer] centos4_x86_64_V4.0 vs. centos4_V4.0 >Xiangchuan Chen, > >The centos4_x86_64_v4.0 version of freesurfer should not use the shared >lib version of libglut, but rather the static version, as the >centos4_v4.0 version does. This is a mistake that will be fixed in the >v4.0.1 release, later this week. Thanks for pointing this out. > >As for tkmedit, do the + and - icons next to the slice number entry box >work? Can you scroll through slices using the up and down arrow keys? >Are you able to enter numbers into the slice number box? > >Nick > > >On Mon, 2007-09-17 at 13:17 -0400, Xiangchuan Chen wrote: >> Hi all, >> >> I had tried to play with FreeSurfer centos4_x86_64_v4.0 on my laptop in the past two days, and found that the tksurfer did not show the brain surface correctly. Today, I installed the centos4_v4.0 on the same laptop. This version seems to work well. The only difference I have noticed by far between these two versions is that the centos4_x86_64_v4.0 needs libglut.so.3, but the centos4_v4.0 does not. Can anybody tell me why this difference makes sense here? >> >> I also found that I could not input the slice # with keyboard in the TKMedit Tools window. Can anybody tell me how I can do that? >> >> My system: >> >> HP NC8430 laptop (ATI X1600 video card) >> Fedora 6 (X86_64) >> >> Thanks in advance, >> >> Xiangchuan Chen >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> ========= End Of Original Message =========

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centos4_x86_64_V4.0 vs. centos4_V4.0
by Xiangchuan Chen 17 Sep '07

17 Sep '07

Hi all, I had tried to play with FreeSurfer centos4_x86_64_v4.0 on my laptop in the past two days, and found that the tksurfer did not show the brain surface correctly. Today, I installed the centos4_v4.0 on the same laptop. This version seems to work well. The only difference I have noticed by far between these two versions is that the centos4_x86_64_v4.0 needs libglut.so.3, but the centos4_v4.0 does not. Can anybody tell me why this difference makes sense here? I also found that I could not input the slice # with keyboard in the TKMedit Tools window. Can anybody tell me how I can do that? My system: HP NC8430 laptop (ATI X1600 video card) Fedora 6 (X86_64) Thanks in advance, Xiangchuan Chen

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thickness and curvature
by Don Hagler 17 Sep '07

17 Sep '07

I see that mris_make_surfaces is normally used to generate thickness and curvature. I would like to generate the ?h.thickness and ?h.curv files without running mris_make_surfaces (I already have white and pial surfaces). Can mris_thickness and mris_curvature (or other programs) give the same results? Those two programs are not heavily documented, so any help on which options to use (to give the same results as mris_make_surfaces) would be appreciated. _________________________________________________________________ Kick back and relax with hot games and cool activities at the Messenger Café. http://www.cafemessenger.com?ocid=TXT_TAGHM_SeptHMtagline1

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qdoc BadMatch error
by Andrew Reid 17 Sep '07

17 Sep '07

Hi, Just installed version 4.0.0 and tried to execute qdec. When I do so I get the following error. Any ideas what it means and how to remedy it? Reading /home/typically/freesurfer/lib/tcl/tkUtils.tcl Using /home/typically/freesurfer/lib/tcl/fsgdfPlot.tcl X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 66 (X_PolySegment) Serial number of failed request: 4721 Current serial number in output stream: 4724 I am using Ubuntu Fiesty. Thanks in advance, Andrew Reid Department of Neurophysiology and Neuroinformatics UMC St. Radboud Nijmegen, The Netherlands

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starting problems
by Thomas Doring 17 Sep '07

17 Sep '07

Hello all, After sucessful installation, i am trying to run FREESURFER. The conversion to 001.mgz seems to work, but when i want to run recon- all i get the following output: recon-all -001 ERROR: Flag -001 unrecognized. -001 Linux localhost.localdomain 2.6.9-55.ELsmp #1 SMP Wed May 2 14:04:42 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Sep 17 09:54:41 BRT 2007 Do i forget something before running recon-all like reorientation etc ? Thanks for help, Thomas

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Subgenual problems
by Alex Fornito 16 Sep '07

16 Sep '07

Hi all, I've been having problems getting accurate surfaces in the subgenual cingulate region, as illustrated in the attached pics. I previously posted to the list about this, and you sent me a newer mris_surf for an older version of freesurfer that fixed the problem in some, but not all cases. It seems like the new version (included with 4.0) is still giving me some grief. Any suggestions re: what I can do? Thanks for your help, Alex (I'm re-posting this query as per Bruce's request last week.) Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia Phone: +61 3 8344 1861 Fax: +61 3 9348 0469 Email: fornitoa(a)unimelb.edu.au www.psychiatry.unimelb.edu.au/mnc

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cluster/peak vertex infomation
by Catherine Alexandra Hartley 16 Sep '07

16 Sep '07

Hi, I have a few questions, the answers to which probably all involve running mri_surfcluster with the correct arguments specified. 1) What is the easiest way to obtain peak vertex information from a given cluster? 2) For a given sig.mgh file, is there a command which outputs a list/text file of all clusters present? 3) Is there a way to restrict the clusters displayed in the sig.mgh file to clusters of a given # of vertices or larger? Thanks in advance for your help! -Cate

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mri_convert problem?
by Jessica Andrews-Hanna 16 Sep '07

16 Sep '07

Hi - Does anyone know if there is a problem with mri_convert used within the context of unpacksdcmdir? When I type the following at the command line (which we've used several times successfully in the past in the Buckner lab): ssh nexlin6 source /space/freesurfer/nmr-std-env cd /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts unpacksdcmdir -src `/usr/pubsw/bin/findsession 070814_4TT00316 | grep PATH | awk '{print $3}'` -targ ../ -cfg 070814_4TT00316_unpack_fsl.cfg -unpackerr I get the following error: mri_convert /space/archive/133/siemens/ TrioTim-35006-20070814-165946-670000/670000-3-1.dcm ..//anat/ 003/070814_4TT00316_mpr003.nii --sdcmlist ..//anat/003/flf -ot nii -- nspmzeropad 3 --in_type siemens_dicom ERROR: mri_convert child killed: segmentation violation Here's some useful information using bugr: --------------------------------------------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.0-20070914 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: nexlin6 SUBJECTS_DIR: /space/sake/3/users/inverse/subjects PWD: /space/nexus/20/users/jandrews/FDN/070814_4TT00316/scripts Thanks very much, Jessica

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