Freesurfer October 2005

freesurfer@nmr.mgh.harvard.edu

49 participants
62 discussions

morph_subject error
by Lars Tjelta Westlye 18 Oct '05

18 Oct '05

Dear all, I'm encountering following error when running morph_subject <subject>. What is wrong? ............. registration took 0.67 hours writing registered surface to ../surf/lh.rh.sphere.reg... /var/lab-data/genetic/id106 /var/lab-data/genetic/id106/scripts /var/lab-data/genetic/id106/scripts ------------------------------------- /var/lab-data/genetic/id106/scripts mris2rgb -o id106.reg -both -c /var/lab-data/genetic/id106/surf/lh.sulc -canon /var/lab-data/genetic/id106/surf/lh.sphere.reg /var/lab-data/genetic/id106/surf/lh.sphere.reg /var/lab-data/genetic/id106/rgb ------------------------------------- using id106.reg as output stem reading canonical coordinates from /var/lab-data/genetic/id106/surf/lh.sphere.reg. Segmentation fault mris2rgb exited with errors [brain@amygdala genetic]$ Also, when typing check_subject <subject> I get the following warnings: _______ [brain@amygdala genetic]check_subject id106 CHECKING SUBJECT id106 WARN: time for rh.orig is older than rh.qsphere WARN: file rh.inflated is not equal in size to rh.smoothwm WARN: file rh.white is not equal in size to rh.smoothwm WARN: file rh.sphere is not equal in size to rh.smoothwm WARN: file rh.pial is not equal in size to rh.smoothwm WARN: file rh.sphere.reg is not equal in size to rh.smoothwm WARN: time for lh.orig is older than lh.qsphere WARN: file lh.inflated is not equal in size to lh.smoothwm WARN: file lh.white is not equal in size to lh.smoothwm WARN: file lh.sphere is not equal in size to lh.smoothwm WARN: file lh.pial is not equal in size to lh.smoothwm WARN: file lh.sphere.reg is not equal in size to lh.smoothwm WARN: file lh.rh.sphere.reg is not equal in size to lh.smoothwm --------- My guess is that these problems are connected? Anyone know how to fix this? I am the using the FS version from june (?) 2005 on this project. Cheers, Lars T .Westlye

4 3

recon-all -autorecon1 failure
by Elizabeth Fenstermacher 17 Oct '05

17 Oct '05

I am having difficulty running mri_watershed within autorecon1 on two scans, visually the orig volumes look completely normal, but mri_watershed exits with intensity-related errors The data I have been trying to run this on is located in /space/krupa/9/users/PPG_STR/Reisa/PPG10/mri /space/krupa/9/users/PPG_STR/Reisa/PPG19/mri recon-all-log error message: mri_watershed T1.mgz brain.mgz ************************************************************ The input file is T1.mgz The output file is brain.mgz If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=127 y=135 z=131 r=101 first estimation of the main basin volume: 4371827 voxels Error w=White Matter =Intensity too high (>240)...valid input ? ERROR: mri_watershed exited with non-zero status Linux node0078 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 i686 i386 GNU/Linux recon-all exited with errors at Wed Oct 12 14:45:26 EDT 2005

1 0

parcellation atlas
by marc ruiz 17 Oct '05

17 Oct '05

2 1

Error with morph_subject
by sbasho＠nmr.mgh.harvard.edu 14 Oct '05

14 Oct '05

Hi, I have been getting an error message when I try to run morph_subject and I was wondering if it has anything to do with my link to the average7 brain. The error message is below: stable2 ####################################### INFO: SUBJECTS_DIR is /autofs/space/tango_001/users/recon_modygp/surina ERROR: cannot find /autofs/space/tango_001/users/recon_modygp/surina/average7/label/lh-avg_ calcarine_sulcus.label ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on tango:/local_mount/space/tango/1 46474056 41683544 2429768 95% /autofs/space/tango_001 ------------------------------------------ recon-all exited with errors at Fri Oct 14 18:26:26 EDT 2005 Any insight would be most appreciated. Thank you! *************************************************************** Surina Basho Department of Radiology MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th Street, CNY 2301 Charlestown, MA 02129-2020 USA sbasho(a)nmr.mgh.harvard.edu ***************************************************************

1 0

Group analysis
by Sunaina Fotedar 14 Oct '05

14 Oct '05

Dear all, Would it be feasible to do a group analysis with the present developmental release of freesurfer on the subjects which were individually analyzed on the previous(old) version of freesurfer? In other words, is the Group analysis module of present version sensitive to the version in which the data was preprocessed/ reconstructed ? Thanks Sunaina Fotedar Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

12 26

make_average_surface
by antao＠itsa.ucsf.edu 14 Oct '05

14 Oct '05

Hi, I jsut generated the average cortical thickness with make_average_surface in two groups. How can I display them? it would be great that there is a color bar to show the cortical thickness. Thanks, Antao

1 0

contour maps
by Irina Sigalovsky 14 Oct '05

14 Oct '05

Hi all, Is it possible to display surfaces (e.g., *.w files) as contour (rather than, say, color) maps in tksurfer? Thanks, Irina

1 0

libtix8.1.8.3.so
by antao＠itsa.ucsf.edu 14 Oct '05

14 Oct '05

Hi, I just upgraded freesurfer, but I can't run tkmedit. the error is the following. How to solve this problem? Thanks [antao@freesurfer subjects]$ tkmedit tkmedit: error while loading shared libraries: libtix8.1.8.3.so: cannot open shared object file: No such file or directory [antao@freesurfer subjects]$ ldd `which tkmedit` linux-gate.so.1 => (0x0091d000) libtix8.1.8.3.so => not found libtk8.4.so => /usr/lib/libtk8.4.so (0x00a06000) libtcl8.4.so => /usr/lib/libtcl8.4.so (0x0095b000) libglut.so.3 => /usr/lib/libglut.so.3 (0x00112000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x0013b000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x00144000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x00618000) libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x00ddd000) libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x00cc0000) libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x0015e000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x001d9000) libgsl.so.0 => /usr/lib/libgsl.so.0 (0x002ad000) libgslcblas.so.0 => /usr/lib/libgslcblas.so.0 (0x00416000) libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x00c2b000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0x05e98000) libz.so.1 => /usr/lib/libz.so.1 (0x00870000) libm.so.6 => /lib/libm.so.6 (0x00844000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x05807000) libc.so.6 => /lib/libc.so.6 (0x00443000) libdl.so.2 => /lib/libdl.so.2 (0x0086a000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x0056d000) libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 (0x006ed000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x0057c000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00de5000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x005d2000) libpthread.so.0 => /lib/libpthread.so.0 (0x005dc000) /lib/ld-linux.so.2 (0x006f6000) [antao@freesurfer subjects]$

3 3

Fwd: public distribution
by Sasha Wolosin 14 Oct '05

14 Oct '05

Oh, sorry, I see now that I need to use ftp to access the files, nevermind my question. >>> Sasha Wolosin 10/14/2005 9:57 AM >>> Dear all, Has the tutorial data been relocated? I cannot find it on https://surfer.nmr.mgh.harvard.edu/pub/dist Many Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

1 0

public distribution
by Sasha Wolosin 14 Oct '05

14 Oct '05

Dear all, Has the tutorial data been relocated? I cannot find it on https://surfer.nmr.mgh.harvard.edu/pub/dist Many Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

1 0

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Freesurfer October 2005