Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

2D to 3D registration
by Susie Heo 02 Dec '08

02 Dec '08

Hello, I would like to register a 2D EPI oblique axial slice to a 3D MPRAGE and am hoping that Freesurfer will help me do this. I have not had any luck with other fMRI software packages. Caveat: Each subject's EPI axial slice was taken parallel to his/her specific hippocampal longitudinal axis and the angle is unknown. Therefore, I have a low-res 2D axial slice at an unknown angle and a high-res 3D MPRAGE. Is Freesurfer capable of finding and applying the appropriate transformation? Specific suggestions would be greatly appreciated. Best, Susie

4 3

Leopard is missing mri_segstats
by Hans Johnson 02 Dec '08

02 Dec '08

It appears that the program mri_segstats is missing under version 4.1 of mac. diff ~/MacLeopard.list ~/Linux64.list 38a39 > /opt/freesurfer/bin/3dvolreg 62a64 > /opt/freesurfer/bin/dmri_poistats 77a80 > /opt/freesurfer/bin/flirt.newdefault.20080811.sch 79a83,84 > /opt/freesurfer/bin/freeview > /opt/freesurfer/bin/freeview.bin 258a264 > /opt/freesurfer/bin/mri_seg_diff 261a268,269 > /opt/freesurfer/bin/mri_segstats > /opt/freesurfer/bin/mri_segstats.verbose 377a386,387 > /opt/freesurfer/bin/mris_wm_volume > /opt/freesurfer/bin/mris_wm_volume.verbose This shows the binaries that are missing in the Freesurfer .dmg file that exists in the Linux64 tar.gz file. In particular, the missing /opt/freesurfer/bin/mris_wm_volume and /opt/freesurfer/bin/mri_segstats are making the most trouble for me. ===================================================================== In addition to the differences in available applications, the versions of VTK and Perl are also different. Linux is using vtk5.2, and Mac is using vtk 5.0. Mac uses Perl 5.8.6, and linux uses 5.8.0. Any help would be appreciated. If I could get the two missing binaries, then I can start working again. Hans -- Hans J. Johnson, Ph.D. Hans-johnson(a)uiowa.edu 278 GH The University of Iowa Iowa City, IA 52241 (319) 353 8587 Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.

3 2

Segmentation Volume Data
by Yuan Xu 01 Dec '08

01 Dec '08

4 3

atlas use
by Nurunisa Neyzi 01 Dec '08

01 Dec '08

Hi, if I want to use an alternative subcortical atlas (and I only have the equivalent of GCA_ALL but not GCA_SKULL), can I just add -gca GCA_ALL to the command line? Is there anything else I need to do? thanks, Nurunisa

2 1

mri_label2vol
by Steinmann, Iris 30 Nov '08

30 Nov '08

Hi Freesurfers, there is a little problem: I load fsaverage in tkmedit and marked with tools-'Configure-Brush-Info...' an area in the volume, then I saved it as a label (newarea.label). I want to create a binary mask with this newarea.label and used mri_label2vol, to have 1 where the label is and 0 where it is not. But it doesnt work...I just get a file (I tried it with nii and bfloat) with only 0 everywere. Is something wrong in my workflow? I hope somebody have an idea... best greetings Iris

2 1

Ubuntu 8.04.1. libexpat? issues
by Paul Greenberg 28 Nov '08

28 Nov '08

Hello, I am trying to run freesurfer on Ubuntu and recon-all fails to finish on the "bert" data set. Here is the output of bugr: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 Debian version: lenny/sid Kernel info: Linux 2.6.24-19-generic x86_64 I have already made a symbolic link to libtiff.so.3 based on previous archive messages using: "ln /usr/lib/libtiff.so.4 /usr/lib/libtiff.so.3" Command Line: recon-all -all -subjid bert New error message: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance bert mris_volmask.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory After looking through some of the new archive posts on similar issues I typed: ldd /usr/local/freesurfer/bin/mris_volmask.bin and received the following output: linux-vdso.so.1 => (0x00007fff4e5fe000) libX11.so.6 => /usr/lib64/libX11.so.6 (0x00007fa045fcf000) libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x00007fa045db6000) libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00007fa045b37000) libvtkpng.so.5.2 => not found libvtksqlite.so.5.2 => not found libvtkzlib.so.5.2 => not found libexpat.so.0 => not found libvtkmetaio.so.5.2 => not found libvtkverdict.so.vtk5.2.0 => not found libvtkHybrid.so.5.2 => not found libvtkRendering.so.5.2 => not found libvtkGraphics.so.5.2 => not found libvtkImaging.so.5.2 => not found libvtkftgl.so.5.2 => not found libvtkIO.so.5.2 => not found libvtkFiltering.so.5.2 => not found libvtkCommon.so.5.2 => not found libvtkDICOMParser.so.5.2 => not found libvtksys.so.5.2 => not found libvtkexoIIc.so.5.2 => not found libvtkNetCDF.so.5.2 => not found libjpeg.so.62 => /usr/lib64/libjpeg.so.62 (0x00007fa045914000) libtiff.so.3 => /usr/lib64/libtiff.so.3 (0x00007fa0456bb000) libz.so.1 => /usr/lib64/libz.so.1 (0x00007fa0454a4000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x00007fa04526c000) libdl.so.2 => /lib/libdl.so.2 (0x00007fa045068000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007fa044e4c000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fa044b41000) libm.so.6 => /lib/libm.so.6 (0x00007fa0448c0000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fa0446b2000) libc.so.6 => /lib/libc.so.6 (0x00007fa044350000) libxcb-xlib.so.0 => /usr/lib64/libxcb-xlib.so.0 (0x00007fa04414f000) libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00007fa043f34000) libXt.so.6 => /usr/lib64/libXt.so.6 (0x00007fa043cd0000) libSM.so.6 => /usr/lib64/libSM.so.6 (0x00007fa043ac8000) libICE.so.6 => /usr/lib64/libICE.so.6 (0x00007fa0438ad000) libXext.so.6 => /usr/lib64/libXext.so.6 (0x00007fa04369c000) /lib64/ld-linux-x86-64.so.2 (0x00007fa0462d2000) libXau.so.6 => /usr/lib64/libXau.so.6 (0x00007fa04349a000) libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x00007fa043295000) I'm not sure what the next step is, and thanks in advance for your help! Paul -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 pgreenberg(a)ucsd.edu -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 pgreenberg(a)ucsd.edu

2 1

shell choice
by Jared Price 28 Nov '08

28 Nov '08

Hello freesurfer gurus, I noticed on the wiki that they recommend using tcsh when running freesurfer, although they say other shells can be used. Is there a significant advantage to using tcsh when running freesurfer? If I would rather use bash is there any significant reason not to? Warmest regards, -Jared

4 3

tksurfer doesn't work
by RafaelHuber＠access.unizh.ch 28 Nov '08

28 Nov '08

Dear Freesurfer Experts I have a Macbook 2GHz Intel Core 2 Duo (MAC OSX Version 10.4.11) and just installed Freesurfer v4.1.0. I followed the installation and setup steps of the freesurfer homepage and everything seemed to work well. When I finally tried the "tksurfer bert rh pial" command I got an error message called: "GLUT: Fatal Error in tksurfer.bin: could not open display: ". Later on I saw, that tksurfer actually works, but only when I type the command into the X11 terminal. Is this correct? Do I always have to work with the X11 terminal, or did I do something wrong? Thanks for your help in advance! Cheers, Rafael Huber

2 1

problem with intensity normalization and mri banding artifacts
by David Qixiang Chen 27 Nov '08

27 Nov '08

Hi all, I'm running into a problem where some of my scans have varied brightness between slices. What happens is that this results in heavy banding of the resulting scans, and this creates major problem for freesurfer to segment out wm because of the variation in signal intensity. Intensity normalization doesn't seem to correct this kind of signal problems. I'm wondering what would be a good way to go about correcting this? I'm been doing control points and wm edits, but because the wm intensity is not standarized across the slices, I think it's just an exercise in futility so far. I've attached a screen shot. Thanks! - David Qixiang Chen

2 3

convert .img to .mgz
by Luke Tseng 27 Nov '08

27 Nov '08

how do i convert a .img file to something i can view in freesurfer like .mgz? mri_convert?

2 1

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