Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

flattening full patch
by Don Hagler 01 Sep '05

01 Sep '05

When I try to do a full flattening of a surface I often get areas with extreme squishing, looking like wrinkles. Usually if I redo the cuts in slightly different ways (e.g. adjust the spacing between cuts, extend the cuts farther onto the lateral surface, etc) I can get the flattened surface to come out looking smooth. Sometimes it takes several attempts (with several hours of computation for each attempt) to get it right. Has anyone else noticed this, and has anyone attempted to improve the flattening algorithm?

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Lib prob?
by Fornito, Alexander 01 Sep '05

01 Sep '05

Hi, We've recently installed the freesurfer-Linux-rh9-dev20050729.tar.gz distribution along with fs_supportlibs.tar.gz. csurf works ok, but if i try to run tksurfer, I get the error message below. We'd appreciate any help as we've been stuck for a while. Thanks! tksurfer 1000027 rh white surfer: current subjects dir: /data/flanders/work/alex/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/flanders/work/alex/freesurfer/subjects surfer: Reading header info from /data/flanders/work/alex/freesurfer/subjects/1000027/mri/T1/COR-.info INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. INFO: Volume /tmp/mritotal_17663/orig_8_dxyz.mnc cannot be found. surfer: vertices=152190, faces=304376 surfer: single buffered window Xlib: extension "XFree86-DRI" missing on display ":0.0". Tix_Init failed: version conflict for package "Tcl": have 8.3, need 8.4 surfer: using interface /usr/local/freesurfer-linux9/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer-linux9/lib/tcl/fsgdfPlot.tcl couldn't load file "/usr/lib/libtix8.1.8.4.so": /usr/lib/libtix8.1.8.4.so: cannot open shared object file: No such file or directorysurfer: Error sending tcl command UpdateUndoItemLabel "Nothing to Undo": invalid command name "UpdateUndoItemLabel" surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OriginalVSetLoaded 1: can't read "glMenuGroups(mg_OriginalVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_InflatedVSetLoaded 0: can't read "glMenuGroups(mg_InflatedVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_WhiteVSetLoaded 0: can't read "glMenuGroups(mg_WhiteVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_PialVSetLoaded 0: can't read "glMenuGroups(mg_PialVSetLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_TimeCourseLoaded 0: can't read "glMenuGroups(mg_TimeCourseLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_OverlayLoaded 0: can't read "glMenuGroups(mg_OverlayLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_CurvatureLoaded 0: can't read "glMenuGroups(mg_CurvatureLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_LabelLoaded 0: can't read "glMenuGroups(mg_LabelLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldSignLoaded 0: can't read "glMenuGroups(mg_FieldSignLoaded)": no such variable surfer: Error sending tcl command tkm_SetMenuItemGroupStatus mg_FieldMaskLoaded 0: can't read "glMenuGroups(mg_FieldMaskLoaded)": no such variable % surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name "MoveToolWindow" surfer: Error sending tcl command MoveToolWindow 663 670: invalid command name "MoveToolWindow"

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global thickness
by Goldman, Aaron (NIH/NIMH) 01 Sep '05

01 Sep '05

Hi, For each of my subjects, I'd like to obtain a global value of their average thickness. What would be the best way to do this? Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: aarong(a)mail.nih.gov <mailto:aarong@mail.nih.gov>

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documentation of matrix format for talairach transform
by Tracy Wang 31 Aug '05

31 Aug '05

Hi all, I was wondering if anyone knows what the format of the matrix in the talairach.xfm file is or if there is any documentation available describing the matrix format. Thanks! Tracy Wang Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang(a)artsci.wustl.edu

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ERROR: MRISeqchangeType
by Daniel Goldman 31 Aug '05

31 Aug '05

I recently received an error I've never seen before at the very end of a call to mri_convert: INFO: set hdr.hist.orient to 'coronal flipped' mri_convert -ot spm -rl /space/windu/4/users/recon//ESWJ78_recon/mri/orig/ /space/windu/4/users/recon//ESWJ78_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz /space/windu/4/users/recon//ESWJ78_recon/mri/32echo/magnitude/t2star_imgs/t2star_params.img reading from /space/windu/4/users/recon//ESWJ78_recon/mri/32echo/magnitude/parameter_maps_average/T2star.mgz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.00513606, -0.981282, 0.192508) j_ras = (-0.0277379, -0.192297, -0.980945) k_ras = (-0.999602, 0.010378, 0.026231) reading template info from volume /space/windu/4/users/recon//ESWJ78_recon/mri/orig/... changing data type from 3 to 0 (noscale = 0)... MRIchangeType: Building histogram ERROR: MRISeqchangeType Any idea as to what the problem might be? Thanks very much, - Daniel Goldman

3 2

OSX or linux for new FS?
by Fred Dick 30 Aug '05

30 Aug '05

Hi Bruce, Doug, et al. I was going to pick up some machines for freesurfer recon purposes - any recommendations on preferred platform? cheers, Fred

2 1

Recon-all followup
by Clifford A. Smith, PhD 30 Aug '05

30 Aug '05

Following Yuan-Fen Kuo¹s suggestion, I added a # at line 275 in recon-all. Recon-all stage1 now proceeds until it crashes with the following: Intensity Normalization Tue Aug 30 12:47:03 CDT 2005 /Users/Shared/freesurfer/subjects/00139/mri mri_normalize orig.mgz T1.mgz reading from orig.mgz... normalizing image... talairach transform 1.131 -0.045 -0.066 0.052; 0.052 1.009 0.210 -10.266; 0.056 -0.234 1.111 -12.367; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 Bus error ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Tue Aug 30 12:48:33 CDT 2005 Any suggestions on proceeding? ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

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converting from ANALYZE 2D format
by Renat Yakupov 30 Aug '05

30 Aug '05

Can FreeSurfer read from ANALYZE 7.5 2D images? I have some brain volumes saved as 2D, a file per each slice. I can probably combine then into a single 3D volume in SPM or something, but I was wondering if FreeSurfer can read them in directly in this form? Thanks. Regards, Renat.

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Recon-all question
by Clifford A. Smith, PhD 30 Aug '05

30 Aug '05

I¹ve installed Freesurfer on Mac running Tiger. Am able to run mri_convert to attain 001.mgz and view with tkmedit without a problem. Can run recon-all help and attain the help files, but running recon-all subjid <subject name> -all (or autorecon1) mgz does not produce any image output only the following: Any suggestions? Thanks. Cliff % [Clifford-Smiths-Computer:shared/freesurfer/subjects] Cliff% recon-all -subjid 00139 -autorecon1 -mgz INFO: SUBJECTS_DIR is /Users/Shared/freesurfer/subjects ######################################## program versions used $Id: recon-all-nmr,v 1.71 2005/07/11 22:46:53 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/progs/rawtominc/rawtominc.c,v 6.13.2.2 2005/03/16 19:02:52 bert Exp $ minctracc.c $Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.11 2004/02/12 05:54:22 rotor Exp $ !p$Header: /software/source/minc/progs/mincresample/mincresample.c,v 6.12.2.1 2005/03/16 19:02:51 bert Exp $ $Header: /software/source/minc/progs/mincaverage/mincaverage.c,v 6.4.2.2 2005/03/16 19:02:49 bert Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ # $Id: nu_estimate.in,v 1.1 2003/04/16 14:29:34 bert Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using mgz format . ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

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mgz format
by Sasha Wolosin 29 Aug '05

29 Aug '05

Sorry to send this twice, but I should have elaborated: I am trying to convert files to mgz format. I was able to run mri_convert, but when I run csurf and attempt to open the orig volume, I get the error: "First orig image: /freesurfer/subjects/2332/mri/orig/COR-001 not found" Does anyone know why this may happen? Here is the command and output: [root@localhost /freesurfer]# cd subjects/2332/mri/orig [root@localhost orig]# ls 2332_analyze 2332_crsg [root@localhost orig]# mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz mri_convert -it dicom -ot mgz 2332_crsg/001 001.mgz reading from 2332_crsg/001... 124 DICOM 3.0 files in list Found 124 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 124. reading DICOM image... ------------------------------------------------- DICOM meta-header file name 2332_crsg/001 Date and time study date 20030630 study time 101639.0000 series time 104735.12 acquisition time 104735.12 Identification patient name ... manufacturer Philips Medical Systems Dimensions number of rows 256 number of columns 256 number of frames 124 pixel width 0.9375 pixel height 0.9375 slice thickness 1.5 field of view 240 image number 1 (might be not reliable) Acquisition parameters echo time 6.00003 repetition time 35 inversion time not found echo number 1 flip angle 0.785398 bits allocated 16 Spatial information first image position -114.756 -101.936 133.356 last image position -126.115 82.1994 135.698 image orientation 0.998088 0.0614863 0.00638348 0.00559035 0.0130627 -0.999899 ------------------------------------------------- TR=35.00, TE=6.00, TI=0.00, flip angle=45.00 i_ras = (-0.998088, -0.0614863, 0.00638348) j_ras = (-0.00559035, -0.0130627, -0.999899) k_ras = (0.0615663, -0.998022, 0.0126937) writing to 001.mgz... [root@localhost orig]# csurf Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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