Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30071 discussions

Re: [Freesurfer] mris_flatten missing 4 lib
by Joongnam Yang 03 Oct '06

03 Oct '06

Dear all, I did occipital cortex flattening and when I tried to display it on tksurfer using "tksurfer average lh occip.patch.flat", I got the following error message, which I have never seen. (the error message on memory) surfer: current subjects dir: /home/nam/AVERAGE surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/nam/AVERAGE/average/surf Loading tal xfm file /home/nam/AVERAGE/average/mri/transforms/talairach.xfm surfer: Reading header info from /home/nam/AVERAGE/average/mri/T1.mgz MRISalloc(16711682, 408): could not allocate vertices Cannot allocate memory Would someone hint at a solution? Nam.

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open patch file?
by xingfeng lee 03 Oct '06

03 Oct '06

Dear FreeSurfer Experts, I tested flatten using mris_flatten, it took 8 hours. I want to see the result of the faltten, but i do not know how to open these patch files, rh.patch rh.patch.flat rh.patch.flat.out could you help to give some suggestions? Thanks in advance. Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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how to save segmentation in analyze format by using command line?
by Shahabuddin Ansari 02 Oct '06

02 Oct '06

Hello, I usually open subcortical segmentations in tkmedit and save the segmentations in analyze format. Is there any command line option to do the same? Appreciate it. Shahab --------------------------------- Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business.

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mris_flatten missing 4 lib
by xingfeng lee 02 Oct '06

02 Oct '06

Dear FreeSurfer Experts, Where can I find and install the missing 4 lib for mis_flatten? libtix8.1.8.3.so => not found libtk8.4.so => not found libgsl.so.0 => not found libgslcblas.so.0 => not found [xingfeng@ambrose bin]$ pwd /usr/local/freesurfer/bin [xingfeng@ambrose bin]$ ldd tksurfer linux-gate.so.1 => (0x55000000) libtix8.1.8.3.so => not found libtk8.4.so => not found libtcl8.4.so => /usr/lib/libtcl8.4.so (0x00a69000) libglut.so.3 => /usr/lib/libglut.so.3 (0x5500f000) libSM.so.6 => /usr/X11R6/lib/libSM.so.6 (0x007e8000) libICE.so.6 => /usr/X11R6/lib/libICE.so.6 (0x007f2000) libXmu.so.6 => /usr/X11R6/lib/libXmu.so.6 (0x00394000) libXi.so.6 => /usr/X11R6/lib/libXi.so.6 (0x0095b000) libGLU.so.1 => /usr/X11R6/lib/libGLU.so.1 (0x009ec000) libX11.so.6 => /usr/X11R6/lib/libX11.so.6 (0x006fb000) libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0x00965000) libgsl.so.0 => not found libgslcblas.so.0 => not found libjpeg.so.62 => /usr/lib/libjpeg.so.62 (0x004a1000) libtiff.so.3 => /usr/lib/libtiff.so.3 (0x074c7000) libz.so.1 => /usr/lib/libz.so.1 (0x007d5000) libm.so.6 => /lib/tls/libm.so.6 (0x006d0000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x07456000) libc.so.6 => /lib/tls/libc.so.6 (0x005b3000) libdl.so.2 => /lib/libdl.so.2 (0x006f5000) libstdc++.so.5 => /usr/lib/libstdc++.so.5 (0x07251000) libXext.so.6 => /usr/X11R6/lib/libXext.so.6 (0x007c5000) libXt.so.6 => /usr/X11R6/lib/libXt.so.6 (0x00101000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00560000) libpthread.so.0 => /lib/tls/libpthread.so.0 (0x0088a000) libXxf86vm.so.1 => /usr/X11R6/lib/libXxf86vm.so.1 (0x008de000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x0059a000) [xingfeng@ambrose bin]$ cat /etc/redhat-release Fedora Core release 2 (Tettnang) [xingfeng@ambrose bin]$ uname -m i686 Thanks for the help in advance. All the best, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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mris_flatten
by xingfeng lee 02 Oct '06

02 Oct '06

Dear FreeSurfer Experts, Could you help for the cortex flatten? I came across the following problem, i do not know how to fix it. [xingfeng@ambrose surf]# ls lh.area lh.defect_labels lh.rh.sphere.reg lh.white rh.defect_chull rh.pial rh.thickness lh.area.pial lh.inflated lh.smoothwm rh.area rh.defect_labels rh.qsphere.nofix rh.white lh.avg_curv lh.inflated.nofix lh.smoothwm.nofix rh.area.pial rh.inflated rh.smoothwm lh.curv lh.orig lh.sphere rh.avg_curv rh.inflated.nofix rh.smoothwm.nofix lh.curv.pial lh.orig.nofix lh.sphere.reg rh.curv rh.lh.sphere.reg rh.sphere lh.defect_borders lh.pial lh.sulc rh.curv.pial rh.orig rh.sphere.reg lh.defect_chull lh.qsphere.nofix lh.thickness rh.defect_borders rh.orig.nofix rh.sulc [xingfeng@ambrose surf]# pwd /usr/local/freesurfer/subjects/frank/surf [xingfeng@ambrose surf]# mris_flatten -w 0 -distances 12 7 lh.patch lh.patch.flat mris_flatten: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory [xingfeng@ambrose surf]# whoami root [xingfeng@ambrose surf]# mris_flatten -w 0 -distances 12 7 lh.patch lh.patch.flat mris_flatten: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory Could you help? All the best, Li __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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How to get subcortical segmentation for the "average" subject
by jorge luis 02 Oct '06

02 Oct '06

Hello all. How can I get a subcortical segmentation for the average subject (the result of make_average_subject)? There is no aseg.mgz file on the corresponding directory I hope it can be used for VOI analysis of functional data. Any help is welcome. In advance Thank you ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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make_average_subject question
by Balaji Lakshmanan 01 Oct '06

01 Oct '06

Hi all, I made an average subject using make_average_subject script. When I looked in to the surf directory there were two different curvature( ?h.curv and ?h.avg_curv) of slightly different sizes. Could anyone plz tell me what is the difference btwn these two files? Also, can I paint these average curvature files on to a single subject using mri_surf2surf OR ?? Thanks in advance, Balaji

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Using different image acquisitions
by Nicolas Cherbuin 29 Sep '06

29 Sep '06

Hello, Is it possible to coregister a combination of T1, T2, and Flair images to obtain better results? Also, is it possible to assess freesurfer's precision by processing separately a T1 and Flair image in the same subjects taken at the same time and comparing their measures? Thanks Nic

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llibglut.so.3 problem
by XJ Kang 29 Sep '06

29 Sep '06

Hi, I installed freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3-full.tar.gz <http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer-Linux-centos4_x86_64-…> on my Redhat Enterprise Linux WS release 3 (64 bit). When I ran the progam tkmedit or tksurfer, the error messages are: tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory The I created links % ln -sf /usr/lib/libglut.so.3.7.0 /usr/lib64/libglut.so.3. Still, I got the same error, although I updated the lib links and even reboot the machine. Any ideas? Thanks. XJ

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Freesurfer and 64 bits Itanium processors
by Nicolas Cherbuin 29 Sep '06

29 Sep '06

Hi I need to process a large number of scans which could take me a lifetime with my current worksation. I could have access to a linux cluster of Itanium 64 bits machines. However, presently a distribution for Itanium processors does not seem to be available. Is there a possibility to have a version compiled for this platform? Thanks Nic

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