Freesurfer November 2008

freesurfer@nmr.mgh.harvard.edu

70 participants
98 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

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4.1.0 on Ubuntu 8.04
by hashiryu 17 Dec '08

17 Dec '08

Dear all, I have installed the version 4.1.0 (centos x86_64) on Ubuntu 8.04 and tried the test commands for tkmedit and tksurfer as in "Testing your FreeSurfer installation. However, the graphics "flashed" when I typed the command and then disappeared. There was no error message on the terminal. The graphics showed up very briefly when I cricked on some places on the screen where the graphics flashed before. I also tried the centos4 32 bit version and the red hat 9 version, but ended up with the same problem. Is anyone having the similar problem? Thank you, Ryu Hashimoto

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Command Not Found
by Christian Lambert 15 Dec '08

15 Dec '08

I'm just starting out with freesurfer. I am using CentOS5 Linux shell on a windows machine using Freesurfer V4.1.0 with the monitor settings on 32bit. I have set up the license file and also configured freesurfer as per the wiki pages: [user@localhost ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME Desktop/freesurfer FSFAST_HOME Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR Desktop/freesurfer/subjects MNI_DIR Desktop/freesurfer/mni Now when I run recon all (using my own data) I get the following error message: Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 INFO: SUBJECTS_DIR is /home/user/Desktop/freesurfer/subjects Actual FREESURFER_HOME /home/user/Desktop/freesurfer Linux localhost.localdomain 2.6.18-92.1.13.el5 #1 SMP Wed Sep 24 19:33:52 EDT 2008 i686 athlon i386 GNU/Linux mri_motion_correct.fsl: Command not found. flirt: Command not found. talairach_avi: Command not found. tkregister2_cmdl: Command not found. nu_correct: Command not found. mri_normalize: Command not found. .... ... .... mris_make_surfaces: Command not found. mris_register: Command not found. mris_anatomical_stats: Command not found. mrisp_paint: Command not found. cp: cannot stat `Desktop/freesurfer/bin/recon-all': No such file or directory /home/user/Desktop/freesurfer/subjects/chris2 mri_watershed: Command not found. I have been through the manual, wiki pages and seached the mailing list extensively but could not find a solution to this problem. I notice one similar thread in 2006 but it never detailed how the problem was solved, but based on that I include the line below: [user@localhost ~]$ ldd 'which mri_convert' ldd: ./which mri_convert: No such file or directory Thanks for any insight you can provide.

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RE: for cortical thickness
by Zhang, Xiaochu (NIH/NIDA) [F] 05 Dec '08

05 Dec '08

Hi, FreeSurfer export, Thank you very much for response! Now, under some export's help, I used to the mri_surf2vol to transfer cortex thickness into nifti. The below line is what I used. mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon --template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii I checked the result and found the voxel outside the gray matter is always zero and in the gray matter is about 0-3. Could you please do me a favor and tell me whether these data is cortex thickness or not? If they are cortex thickness, why are they always different. In my mind, it should be same in one direction because we calculate the distance between the white matter line and the gray matter line. Thanks a lot! All the best, Xiaochu

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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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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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Segmentation Volume Data
by Yuan Xu 01 Dec '08

01 Dec '08

4 3

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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Freesurfer November 2008