Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Error with motion-correction session(ms-sess)
by 卯野賢太 02 Dec '08

02 Dec '08

Hi, Mr or Ms My name is Kenta in Japan. I'm undergraduate student. Please help me! I've tried some things to solve the error with mc-sess. But I could not solve this error. The mc-sess processing didn't completely run and following message showed up. I'm using matlab R2007a, macOS10.5.5, and freesurfer ver4.0.5. If you want some information about this error or another things, let me know. ========================================================== ->> >> >> >> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2008-12-02 20:08:06.237 MATLAB[1256:60b] Process manager already initialized -- can't fully enable headless mode. ========================================================== Yours sincerely. Kenta

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Using qdec to compare groups of twins?
by Burmicz, Ryzarda 02 Dec '08

02 Dec '08

Hello, Could you please advise as to whether or not the following analysis is suitable? I would like to compare groups of monozygotic twins (MZ concordant vs. MZ control ; MZ discordant affected twin vs. unaffected twin) using qdec. This is not as straightforward as group comparisons usually are because I cannot make the assumption of all data being independent as twin pairs are, obviously, related to one another. To get around this issue I have started a qdec analysis and added a category 'pair' in which twin pairs share a category as follows (qdec.table.dat), in order to indicate that they have shared genetic and environmental influence: subject no subjid pair diagnosis age gender 1 a MZ_Discord_Well ... ... 2 a MZ_Discord_Ill 3 b MZ_Discord_Ill 4 b MZ_Discord_Well 5 c MZ_Discord_Well 6 c MZ_Discord_Ill 7 h MZ_Discord_Well 8 h MZ_Discord_Ill 9 l MZ_Discord_Well 10 l MZ_Discord_Ill 11 m MZ_Discord_Well 12 m MZ_Discord_Ill 13 n MZ_Discord_Well 14 n MZ_Discord_Ill 15 p MZ_Discord_Well 16 p MZ_Discord_Ill 17 s MZ_Discord_Well 18 s MZ_Discord_Ill 19 t MZ_Discord_Well 20 t MZ_Discord_Ill I would appreciate if you could suggest a more robust way around this. Many thanks, Rysia

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design matrix : inter-run effetcs
by Andersson Frederic 02 Dec '08

02 Dec '08

Hi, Computing individual fMRI analysis (several runs) and looking at the design matrix (X.mat), I saw that only one regressor represents each condition. I was expecting that the number of regressors concerning a condition would be the number of runs (as SPM). There are "inter-run effect" regressors but is this better if I affect a different value for each of run and each condition (see examples below). Other question concerning design matrix : only 3 movement parameters included in the design matrix. Why 3 rather than the 6 computed during movement correction? Concerning inter-run effects and movement parameters, is there any advantage of reducing the number of regressors but having a less ideal model? >>> 1 condition = 1regressor 0 = rest 1=conditionA 2=conditionB Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 1 15 1 18 1 18 1 18 1 21 1 21 1 21 1 24 1 24 1 24 1 27 1 27 1 27 1 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 2 42 2 45 2 45 2 45 2 48 2 48 2 48 2 51 2 51 2 51 2 54 2 54 2 54 2 57 0 57 0 57 0 >>> 1 condition = 1regressor / run 0=rest 1=conditionA run#1 2=conditionB run#1 3=conditionA run#2 4=conditionB run#2 5=conditionA run#3 6=conditionB run#3 Pardagim files : RUN#1 RUN#2 RUN#3 0 0 0 0 0 0 3 0 3 0 3 0 6 0 6 0 6 0 9 0 9 0 9 0 12 0 12 0 12 0 15 1 15 3 15 5 18 1 18 3 18 5 21 1 21 3 21 5 24 1 24 3 24 5 27 1 27 3 27 5 30 0 30 0 30 0 33 0 33 0 33 0 36 0 36 0 36 0 39 0 39 0 39 0 42 2 42 4 42 6 45 2 45 4 45 6 48 2 48 4 48 6 51 2 51 4 51 6 54 2 54 4 54 6 57 0 57 0 57 0 Frédéric ANDERSSON.

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question on tksurfer tcl
by j janssen 02 Dec '08

02 Dec '08

Hi, using version 4.0.5 my goal: to display in tksurfer an inflated brain with curvature and an *outlined* label, using a tcl-script. there are probably numerous ways, i did: tksurfer "subject" rh inflated -gray -tcl tksurf.tcl where tksurf.tcl contains: make_lateral_view rotate_brain_x -90 redraw labl_load "label-file" set gaLinkedVars(redrawlockflag) 0 SendLinkedVarGroup redrawlock set gaLinkedVars(labelstyle) 1 SendLinkedVarGroup view save_tiff "tiff_file.tiff" all works except for the label to be outlined. any suggestions? thanks! -joost

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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

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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

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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

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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

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