Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30057 discussions

FreeSurferEnv.sh problems
by Sebastian Moeller 01 Mar '06

01 Mar '06

Dear All, my copy of freesurfer-Linux-centos4_x86_64-dev20060224-full contains a small error in the file FreeSurferEnv.sh. In line 155 "export =$MNI_INSTALL_DIR/data" should read "export MNI_DATAPATH=$MNI_INSTALL_DIR/data". Ahoi Sebastian "friend of bash" Moeller -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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FS-FAST spatialsmooth-sess error
by raij＠nmr.mgh.harvard.edu 28 Feb '06

28 Feb '06

Hi Doug, spatialsmooth-sess failed on the second run (out of 6 runs) with the output: ... ERROR: failure writing /tmp/ipfsl_19705/fmc.img as volume type 16 /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT/bold mri_convert 005/fmc.bhdr /tmp/ipfsl_19705/fmc.img --out_type analyze4d ERROR: mri_convert failed ERROR: ipfsl failed Two explanations come to mind: A. Each number has a different number of TRs. Does the ntrs value in the seq.info (inside bold dir) have to match the actual number of TRs in each run? I here tried to smooth all runs in one step... obviously this is not going to work if the ntrs value has to be correct. Should I process the runs one at a time with -fsd NNN and adjust the seq.info ntrs value between? B. The number of images was big = 666 / 1095 / 1741 per run (2 runs each size). Did the scratch disk or mri_convert run out of memory? *** Detailed problem report: *** on machine ai source /usr/local/freesurfer/nmr-dev-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri cd /space/cognito/21/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT which mc-sess /usr/local/freesurfer/dev/fsfast/bin/spatialsmooth-sess spatialsmooth-sess -sf sessid -df sesspar -fwhm 6 -i fmc -o ifmcsm6 ------------------------------------------------ ------------------------------------------------ /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT Tue Feb 28 18:50:28 EST 2006 /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT/bold /space/cognito/21/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT RunList 004 005 006 009 010 011 ---------------------------------------------- /autofs/space/cognito_021/users/raij/avml_fmri_mctogether/avml19_session_BRISI13_ISI1TR_BERT/bold ... Notice that I am using the building 120 "cognito" installation where: /usr/local/feeesurfer = /space/cognito/24/opt/freesurfer/centos4.0 Thanks, Tommi

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Re: Re: [Freesurfer] activation levels of each voxel
by Joongnam Yang 28 Feb '06

28 Feb '06

Thanks for the answer, > If you want to create statistical maps in surface space, then use > mris_preproc to assemble the data. Then use one of the FSL tools to > do stats or use mri_glmfit Where could I get mris_preproc and mri_glmfit? Google displays nothing on those two functions.....^_^ > You cannot do corrections for mult comparisons > on the surface with the fSL tools. I wanted to know if it's possible to pinpoint a data point corresponding to a particular voxel. If I can do that, I want to do statisitcal test of my own. You mean it's not possible? I mean, 'is it not possible to match each voxel with each data point in the data file?' Nam.

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cannot locate talairach.xfm
by Darren Weber 28 Feb '06

28 Feb '06

I have some path problems when using tksurfer, eg dnlweber:/data/freesurfer/subjects> tksurfer -ucsf_cj rh inflated surfer: current subjects dir: /home/dweber/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/freesurfer/subjects can't find talairach file '/home/dweber/freesurfer/subjects/ucsf_cj/mri/T1/COR-.info/../transforms/talairach.xfm' surfer: Reading header info from /home/dweber/freesurfer/subjects/ucsf_cj/mri/T1/COR-.info INFO: NOT fixing vertex area surfer: vertices=154539, faces=309074 can't find talairach file '/home/dweber/freesurfer/subjects/ucsf_cj/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' surfer: single buffered window surfer: using interface /home/dweber/freesurfer/home/lib/tcl/tksurfer.tcl Reading /home/dweber/freesurfer/home/lib/tcl/tkm_common.tcl Reading /home/dweber/freesurfer/home/lib/tcl/tkm_wrappers.tcl Reading /home/dweber/freesurfer/home/lib/tcl/fsgdfPlot.tcl Reading /home/dweber/freesurfer/home/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl The .xfm file exists, ie dnlweber:/data/freesurfer/subjects> ls ucsf_cj/mri/transforms/ talairach.xfm So the question is, how can I work around this failure to find the talairach.xfm file? Do I need to edit the tksurfer.tcl script? It seems to have a strange way of using relative paths (..) to find the talairach.xfm file. In case it makes any difference, this is my set up: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/dweber/freesurfer/home FSFAST_HOME /home/dweber/freesurfer/home/fsfast SUBJECTS_DIR /home/dweber/freesurfer/subjects FUNCTIONALS_DIR /home/dweber/freesurfer/sessions MINC_BIN_DIR /home/dweber/freesurfer/home/mni/bin MINC_LIB_DIR /home/dweber/freesurfer/home/mni/lib PERL5LIB /home/dweber/freesurfer/home/mni/lib/perl5/5.8.0 GSL_DIR /home/dweber/freesurfer/home/lib/gsl QTDIR /home/dweber/freesurfer/home/lib/qt TCLLIBPATH /home/dweber/freesurfer/home/lib/tcltktixblt/lib FSL_DIR /usr/local/fsl where the /home/dweber/freesurfer contains symlinks (please don't ask me why), eg: dnlweber:/data/freesurfer/subjects> ls -l /home/dweber/freesurfer/ total 0 lrwxrwxrwx 1 dweber dnl 25 2006-02-24 20:26 functionals -> /data/freesurfer/sessions lrwxrwxrwx 1 dweber dnl 21 2006-02-24 20:26 home -> /usr/local/freesurfer lrwxrwxrwx 1 dweber dnl 25 2006-02-24 20:26 sessions -> /data/freesurfer/sessions lrwxrwxrwx 1 dweber dnl 25 2006-02-24 20:26 subjects -> /data/freesurfer/subjects -- Darren L. Weber, Ph.D. Visiting Postdoctoral Scholar Dynamic Neuroimaging Laboratory, Department of Radiology, University of California, San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." --Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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activation levels of each voxel
by Joongnam Yang 28 Feb '06

28 Feb '06

Hi all, When I overlay functional data (e.g. from FSL) onto a Freesurfer-produced inflated brain, I see the activations shown in colors. I want to pick a voxel in Talairach coordinates in those activations and see how the particular voxel's activation level changes throughout different data sets of the same brain. So, my question is how can I get the activation level of a particular voxel consistently throughout different data sets, so that I can do some sort of statistical tests? Thanks in advance. Nam.

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Question: FS-FAST mc-sess -perrun
by raij＠nmr.mgh.harvard.edu 28 Feb '06

28 Feb '06

Hi Doug, The issue is motion correction in FS-FAST. The environment is nmr-dev-env. mc-sess flag -perrun is documented like this: "MC each run separately (targ=mid)". 1. Does "targ=mid" implicate that the target, within each run, is the image half way through the run? 2. Does this equal to using the mc-sess -rlf runlistfile flag, and changing the contents of the runlistfile to match each of the run numbers, one at a time? Thanks, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. raij(a)nmr.mgh.harvard.edu

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mri_motion_correct2 woes
by Sebastian Moeller 28 Feb '06

28 Feb '06

Dear All, I encounter some problems with mri_motion_correct2. I scanned 10 structurals of a monkey that was not moved or moving during the whole scan time. Now I expect mri_motion_correct2 to produce nice averages of my ten runs, but it insists upon displacing/rotating some of my scans. That is in one "beautiful" example a single run's volume was turned by 90 degrees. Are there any expert options for mri_motion_correct2 to clue it in on the expected scan quality? A before I forget centos4_x86_64-dev20060224 is the version I am trying. Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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mris_fix_topology update
by Sebastian Moeller 28 Feb '06

28 Feb '06

Hi All, some more details to the segfault. The critical program is mris_fix_topology, which allocates around 3.7GB of memory and hogs the CPU for at least an hour, then while holding around 3.6GB goes into D state (as seen by top) and then after some time segfaults with the error code 4. Error code 4 most likely means (on Linux x86_64) user_mode page_not_found on read. If I can help debug this I would be happy to. Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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mri_fix_topology segfaults
by Sebastian Moeller 28 Feb '06

28 Feb '06

Dear All, the stage Suse Linux 9.3 x86_64 on AMD Opteron, the players freesurfer-Linux-centos4_x86_64-dev20060224-full, especially mri_fix_topology, the play segfault while trying to correct defect 0. Is there any way I can help to debug this issue, or is my system just beyond help? Ahoi Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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autoreg-sess and spmregister-sess problem
by Reza Rajimehr 27 Feb '06

27 Feb '06

Hi, In the FS-FAST analysis stream (dev environment), I used autoreg-sess command as follows: autoreg-sess -s mvp022106 -df df.txt It successfully generated a register.dat file in the bold directory. Then I used tkregister-sess as follows: tkregister-sess -s mvp022106 -df df.txt -rsd t1epi When tkregsiter window comes, the structural volume (anatomical T1) is OK but t1epi volume is completely corrupted. However, running tkregister-sess with '-rsd t1epi' generates another register.dat file in the directory above the bold directory. When I use this register.dat file in the tkregister-sess command, t1epi volume looks fine and almost in the appropriate location as T1 volume. I also tried spmregister-sess instead of autoreg-sess: spmregister-sess -s mvp022106 -df df.txt -fsd bold A register.dat file is generated by this command in the bold directory. Then I used tkregister-sess as follows: tkregsiter-sess -s mvp022106 -df df.txt -fsd bold In the tkregsiter window, the functional volume looks fine but it is largely displaced. I could finally register it manually. I might do something wrong with autoreg-sess and spmregister-sess or is there a bug for these commands? Thanks, Reza ******************************** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: reza(a)nmr.mgh.harvard.edu ********************************

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Freesurfer