Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

(no subject)
by hankee 16 May '07

16 May '07

hi, I don't know the procedure of the FreeSurfer? Although the recon-all illustration contains lots of the steps, I don't know the meaning. So I want to know the brief step about the FreeSurfer how to deal with 3D data? Thank you very much hankee，duhanjian(a)sohu.com 2007-05-05

1 0

parcellation issues
by Bagnato, Francesca (NIH/NINDS) [E] 15 May '07

15 May '07

Dear Users: I would like to ask how to treat the data of a subject for whom segmentation worked alright but the parcellation looks like the one I am herein attaching. Thanks, Francesca Francesca Bagnato, MD-PhD Staff Scientist, NIB-NINDS-NIH Building 10, Room 5S205 9000 Rockville Pike Bethesda, MD, 20892-1400 MSC Phone #: (301) 594-1415 Fax #: (301) 402-0373

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intergroupavg-sess did not create a sig.bhdr file
by Avram Holmes 15 May '07

15 May '07

To anyone not outside enjoying the nice weather, I have recently completed running intergroupavg-sess intergroupavg-sess -analysis taumax30_stc_smooth6 -contrast Rcue_v_Ncue -group1 LowTrauma -group2 HighTrauma -intergroup LowTrauma_v_HighTrauma -space tal Only 'minsig' and 'sig' files were generated. However, no sig.bhdr files were created. I just wanted to check to see if everything is as it should be. Also, when I run tkmedit-sess in an attempt to view the data on both the between and within group (where all the normal files were created) analyses... tkmedit-sess -analysis taumax30_stc_smooth6 -s LowTrauma_v_HighTrauma -isxavg random -contrast Rcue_v_Ncue -space tal -d . I recieve the following error... -------------------------------------------------------------- tkmedit-sess logfile is /Raid/shared/exp/REfMRI/fMRI_FPPREW/functional/log/tkmedit-sess.log -------------------------------------------------------------- setenv SUBJECTS_DIR /exp/REfMRI/fMRI_FPPREW/structural/ INFO: Found session in: ./LowTrauma_v_HighTrauma INFO: LowTrauma_v_HighTrauma is a group average INFO: Found session in: ./LowTrauma_v_HighTrauma INFO: LowTrauma_v_HighTrauma is a group average INFO: subject is talairach INFO: subject is talairach ERROR: subject talairach does not exist in data base SUBJECTS_DIR: /exp/REfMRI/fMRI_FPPREW/structural/ Do I have to take any steps to add the talairach brain to my studies 'structural' folder so that I can use tkmedit-sess or is this error related to something else. Thanks in advance for any help you can offer, Avram ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Topological defects
by Juergen Haenggi 15 May '07

15 May '07

Dear Freesurfer users Is there any rule of thumb with respect to the size of topological defects? Sometimes large defects (involving more than 10000 or 20000 vertices) occur and the topological correction for these defects runs more than 48 hours and sometimes failed to correct them. How long should I wait? Up to which number of vertices involved in a defect I should accept it or manually edit it? Thanks a lot for help Best regards Juergen --------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ---------------------------------------------------------------------------

2 1

binary masks: 1 output file per aseg label
by Juranek, Jenifer 14 May '07

14 May '07

I'm interested in parsing aseg.mgz into separate binary mask files for each aseg label. Is this possible? The closest topic I found was located at the following URL: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFu nctionalSpace 2.0 Creating binary masks The segmentation for a particular structure can be extracted to create a binary mask (i.e., a volume where the voxel value is 1 if it is in the structure and 0 otherwise). To make a binary mask of the left putamen, which has been assigned label 12 (see ${FREESURFER_HOME}/FreeSurferColorLUT.txt), use the following command: avwmaths ./fbert.feat/reg/freesurfer/aparc+aseg.nii.gz \ -thr 12 -uthr 12 \ ./fbert.feat/reg/freesurfer/lh.putamen.nii.gz I checked the following for additional help...but still need some help... http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands Many Thanks, Jenifer

4 3

reg-feat2anat regsitration problems
by oxro03＠yahoo.com 14 May '07

14 May '07

Hi Doug & others, I am trying to use reg-feat2anat as it is described on the FSL web page: http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html However, I always seem t get a very bad registration. I tried using different values for --maxangle --cost mutualinfo --bins, but maintained --dof always at 6 for rigid body registration of the T1 and EPI, but didn't gt any good results. Initially I thought it might be because reg-fea2anat does not use a skull-stripped T1, but when I run Feat using the T1.mgz (converted to .nii.gz) as the main structural image for Registration (and the MNI brain as standard space), both with 'Full Search' option and dof = 6, the registration (with FEAT) works well. Is there anything else I can try to make it work with reg-feat2anat. Why wouldn't the registration work on my data with reg-feat2anat given that it works with Feat? Any comments or suggestions would be very appreciated. best, Sandy --------------------------------- Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out.

2 1

surf-sess error
by Lee, Jung Min 14 May '07

14 May '07

Hi, I was able to use surf-sess command (modified in our group) to take pictures (rgb) of the brain; however, several days ago, I was kept getting errors (even errors with commands that worked fine before). it keep saying tksurfer.new: Command not found., then quit. Would you help me out? Machine: Roma /space/roma/1/users/caplan/plaus2 Env: Standard environment Subjects_Dir: /space/thor/1/users/west/subjects [roma:plaus2] (nmr-std-env) /space/roma/1/users/caplan/plaus2/scripts/surf-sess-rgb_wfile \ ? -analysis plaus2_corr \ ? -space sph \ ? -spacedir sph20 \ ? -subject west_margaret \ ? -s isxavg-plaus2_corr \ ? -contrast implaus_plaus_8-12sum \ ? -map sig \ ? -fthresh 1.3 \ ? -fmid 2.0 \ ? -fslope 1 \ ? -df dir \ ? -isxavg random \ ? -avgcurv \ ? -offset 0 \ ? -wfile /space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm in16_minarea300_lh_o.w \ ? -hemi lh \ ? -rgbname plaus2_corr_implaus_plaus_8-12sum_300 cat: /usr/local/freesurfer/stable/fsfast/docs/version: No such file or directory ----------------------------------------------------------------- surf-sess logfile is /dev/null ----------------------------------------------------------------- ---------->>>>>>>>>>>....<<<<<<<<<<<<-------------------- INFO: You are about to use the NEW version of tksurfer. INFO: If you want to use the OLD version, re-run surf-sess INFO: with the -old flag. ---------->>>>>>>>>>>....<<<<<<<<<<<<-------------------- ------------------------------------------------------ ------------------------------------------------------ Session: isxavg-plaus2_corr ---- ------ lh hemisphere ------ sig-0-west_margaret west_margaret nowsource west_margaret equal wfile is /space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm in16_minarea300_lh_o.w ------------ tcl file ----------- set val /space/roma/1/users/caplan/plaus2/cluster_13new/implaus_plaus_8-12sum_clth13_thm in16_minarea300_lh_o.w sclv_read_binary_values 0 set curv lh.avg_curv read_binary_curv; set curvflag 1; source /usr/local/freesurfer/stable/lib/tcl/readenv.tcl file mkdir /autofs/space/roma_001/users/caplan/plaus2/rgb file mkdir /autofs/space/roma_001/users/caplan/plaus2/rgb open_window sclv_set_current_field 0 puts "Taking Snapshots..." make_lateral_view redraw set rgb /autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum _300_lh_lat.rgb save_rgb rotate_brain_x 90 redraw set rgb /autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum _300_lh_ven.rgb save_rgb make_lateral_view rotate_brain_y 180 redraw set rgb /autofs/space/roma_001/users/caplan/plaus2/rgb/plaus2_corr_implaus_plaus_8-12sum _300_lh_med.rgb save_rgb exit --------------------------------- ---------------------------------------------------------- /autofs/space/roma_001/users/caplan/plaus2/isxavg-plaus2_corr/bold/plaus2_corr/s ph20-rfx/implaus_plaus_8-12sum tksurfer.new -west_margaret lh inflated -tcl /tmp/surf-sess-22861.tcl ---------------------------------------------------------- tksurfer.new: Command not found. Mon May 14 12:43:08 EDT 2007 I am also attaching the /surf-sess-rgb_wfile under command line. Thanks a lot! -Jung Min ********************************************** Jung Min Lee Neurology/Neuropsychology Martinos Center for Biomedical Imaging Massachusetts General Hospital Tel: 617-726-0303 (work) 617-780-1900 (cell) e-mail: jlee63(a)partners.org <mailto:jlee63@partners.org> jmlee(a)nmr.mgh.harvard.edu <mailto:jmlee@nmr.mgh.harvard.edu> **********************************************

2 2

can't load sig.mgh in dev tksurfer
by Catherine Hartley 14 May '07

14 May '07

Hi, I'm having a problem with the development version of tksurfer. When I try to load a sig.mgh file as an overlay, I get the following error: % surfer: couldn't load /Applications/freesurfer/subjects/reruns/ glmleft/ReappCSplusContrast/sig.mgh sclv_read_from_volume: error in FunD_New Thanks, Cate

3 4

question about 'mris_wm_volume: error while loading shared libraries: libstdc++.so.6'
by Ruiwang Huang 14 May '07

14 May '07

Dear All I meet a problem when I run the command mris_wm_volume to calculate the white matter volume for each hemisphere. The error message is coplied here >> mris_wm_volume >> mris_wm_volume: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory Does any one know how to solve the problem? (My PC installed Suse9.3) Many thanks in advance Rhuang

2 6

reg- feat2anat error
by Furlong, Carolyn 14 May '07

14 May '07

Hi, When I try to register my functional data to anatomical data using reg-feat2anat --feat feat_directory --subject subject_name I get the following error message ERROR: could not read ///example_func.nii.gz as 24 What does this mean? And how can I fix this? Best wishes Carolyn

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Freesurfer