Freesurfer November 2009

freesurfer@nmr.mgh.harvard.edu

92 participants
135 discussions

recon-all exited error
by Jesse Bledsoe 29 Nov '09

29 Nov '09

Hello Experts, I am getting the following error: mri_watershed Error: GLOBAL region of the brain empty ! Linux circ.psy.msu.edu 2.6.9-67.0.4.ELsmp #1 SMP Fri Jan 18 05:00:58 EST 2008 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sat Nov 28 13:29:41 EST 2009 I do not seem to be getting this error with the other files. Any suggestions? Thanks so much, Jesse

2 6

a question about the output template by make_average_subject
by Guang Zeng 29 Nov '09

29 Nov '09

hi, there, I called FS command make_average_subject to create an average subjects using 10 subjects. After the process finished, I found that there are two output template file, "lh.reg.template.tif" and "rh.reg.template.tif". How are these two templates different from the template I built by following the steps described in FS WIKI, The Surface Registration Process; Templates,http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates Thanks a lot! Guang _________________________________________________________________ Bing brings you maps, menus, and reviews organized in one place. http://www.bing.com/search?q=restaurants&form=MFESRP&publ=WLHMTAG&crea=TEXT…

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skull strip errors ?...
by Gonzalo Rojas Costa 28 Nov '09

28 Nov '09

Hi: I am sending attached two images with some skull strip errors that I got in a study... Will I got any error as a result of that skull strip algorithm errors, or I must adjust the parameters of the watershed algorithm ?... Sincerely, Gonzalo Rojas Costa --

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mris_anatomical_stats - how do output measures relate to each other ?
by Samantha Clark 28 Nov '09

28 Nov '09

Hi All, I have a very basic question. Could you please point me to a publication or relevant material that describes the relationship of the various parameters that mris_anatomical_stats outputs. To be precise, I wanted to know how measures like thickness, volume, area, curvature are related. Also, would these measures vary when done on a volume based level in comparison to a surface based approach ? Thank you, Sam

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skull strip errors ?...
by Gonzalo Rojas Costa 27 Nov '09

27 Nov '09

Hi: I am sending attached to images with some skull strip errors that I got in a study... Will I got any error as a result of that skull strip algorithm errors, or I must adjust the parameters of the watershed algorithm ?... Sincerely, Gonzalo Rojas Costa

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problems on virtual machine
by liyari5018 27 Nov '09

27 Nov '09

Dear freesurfer users: I don't know how to read my data in virtual system. When I tried to mount the local disk into virtual system, it asked for root authentication. Do you guys know about the password for root? LJ

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Problem with recon-all on the tutorial data (bert)
by L 27 Nov '09

27 Nov '09

Dear Freesurfers, I have had a problem when running recon-all on your tutorial data (bert). Please find following the content of recon-all.log: *$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $* * $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $* *MRISread(../surf/lh.inflated): could not open file* *No such file or directory* *mris_sphere: could not read surface file ../surf/lh.inflated* *No such file or directory* *Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux* * * *recon-all exited with ERRORS at Fri Nov 20 17:32:05 EST 2009* I suspected that the problem occurred at “mri_ca_register” and reran it as following: *mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z* * * It said the following at the end of the process and “talairach.m3z” could not be found in dir “transforms/” *…* *0621: dt=0.056000, rms=0.414 (0.016%), neg=0, invalid=3625* *0622: dt=0.056000, rms=0.414 (0.020%), neg=0, invalid=3625* *0623: dt=0.056000, rms=0.414 (0.005%), neg=0, invalid=3625* ** *writing output transformation to transforms/talairach.m3z...* *Segmentation fault* * * Here is what given by “bugr” command: *FREESURFER_HOME: /usr/local/freesurfer* *Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0* *Debian version: 5.0 * *Kernel info: Linux 2.6.28-11-generic i686* I am running the VirtualBox Ubuntu version. I have looked at previous posts but have not been able to figure out an appropriate answer to my problem. Any of your help would be highly appreciated. Thank you. Kind regards, Long

3 2

script to check multiple cases with tksurfer
by Mehul Sampat 25 Nov '09

25 Nov '09

Hi Folks, I would like to visually check the cortical parcellation for a large number of patients (>200) using tksurfer. Is there a script to which I could submit a list of subject id's and get it to launch tksurfer and display the parcellation data for each subject sequentially ? Thanks Mehul

4 3

Recon-all -long
by Jürgen Hänggi 25 Nov '09

25 Nov '09

Dear FS experts Am I right that the input for step 3 in recon-all -long are the already cross-sectionally processed images from step 1 and not the raw images that I used to create these cross-sectionally images? Thanks for clarification Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 1

talairach failure
by Ritobrato Datta 24 Nov '09

24 Nov '09

Hello All, I ran recon-all on a subject and got the following error -------------------------------------------- talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Nov 19 16:17:54 EST 2009 /jet/subjects/MC/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) recon-all exited with ERRORS at Thu Nov 19 16:17:55 EST 2009 =======================END LOG FILE======================= The brain is quite rotated from upright alignment, which is likely the problem. Any suggestions on how to do it or whether I should ? Thanks Ri

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Freesurfer November 2009