Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

parcellation
by Wan Park 06 Apr '05

06 Apr '05

Hi, after doing the parcellation and listing the areas with mris_anatomical_stats I have noticed that in many brains (or hemispheres) there are typically two areas that are frequently missing: S_paracentral S_intracingulate is there any explanation for this? is there any way to avoid this? thanks! wan

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aseg skull strip failed
by Michele Perry 05 Apr '05

05 Apr '05

What is the best way to correct an aseg when non-brain regions (eg the skull) are labelled?

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subject averaging
by orphoebe＠polyu.edu.hk 05 Apr '05

05 Apr '05

Hi, I used the following script in the old post to do the subject averaging of the surfaces. However, the 'T1' and 'orig' sub-directory under 'mri' of the 'average' are empty. Is there any way that I can convert the surface file (e.g. rh.orig) into CORs so that I can view the corresponding brain volume using TkMedit? Thanks, Phoebe. ********************************************************** #!/bin/tcsh -ef set SUBJECTS = (031204_wwk 031204_yts 040115_llk 040219_wly) # set SUBJECTS=($SUBJECTS) set average_subject=average if (-e $SUBJECTS_DIR/${average_subject} == 0) then mksubjdirs $SUBJECTS_DIR/${average_subject} else mkdir -p $SUBJECTS_DIR/${average_subject}/surf endif foreach hemi (lh rh) foreach s (orig white pial inflated) set echo=1 mris_make_average_surface -i 7 -o $s $hemi ${s}_avg sphere.reg ${average_subject} $SUBJECTS unset echo end cd $SUBJECTS_DIR/${average_subject}/surf pwd mris_smooth -n 5 ./${hemi}.white_avg ./$hemi.smoothwm mris_inflate ./${hemi}.smoothwm ./${hemi}.inflated mris_curvature -a 10 -w ./${hemi}.white_avg cp ${hemi}.white_avg.H ${hemi}.curv cp $CSURF_DIR/average/$hemi.sphere.reg . ln -s -f $hemi.sphere.reg $hemi.sphere set echo=1 mris_average_curvature -o $average_subject curv $hemi sphere.reg $SUBJECTS ./${hemi}.curv mris_average_curvature -o $average_subject sulc $hemi sphere.reg $SUBJECTS ./${hemi}.sulc mris_average_curvature -o $average_subject thickness $hemi sphere.reg $SUBJECTS ./${hemi}.thickness end cp $SUBJECTS_DIR/$SUBJECTS[1]/mri/T1/COR-.info $SUBJECTS_DIR/${average_subject}/mri/T1 --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor The Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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missing aparc.annot in 'labels' directory
by orphoebe＠polyu.edu.hk 04 Apr '05

04 Apr '05

Hi, I just found out that I forgot to link average7 when I did the 'recon-all' on two subjects' brain data. Will it affect the talairach coordinates? Do I need to do the brain inflation again? Also, I found that the label files, e.g. lh.aparc.annot and rh.aparc.annot, which are expected to be in the 'labels' sub-folder of the subject directory. Is there any way that I can generate these labels files again? Thank you for your help in advance. Phoebe --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor The Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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Re: [Freesurfer] missing aparc.annot in 'labels' directory
by orphoebe＠polyu.edu.hk 04 Apr '05

04 Apr '05

Hi Bruce, I would like to read the anatomical labels with the corresponding Tal coordinates on tksurfer. However, the aparc.annot files are missing in the 'labels' sub-directory of each of the subjects. How can I regenerate them again? Thanks, Phoebe ---- Original message ---- >Date: Mon, 4 Apr 2005 14:39:04 -0400 (EDT) >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] missing aparc.annot in 'labels' directory >To: orphoebe(a)polyu.edu.hk >Cc: freesurfer(a)nmr.mgh.harvard.edu > >Hi Phoebe, > >you shouldn't have to redo any of that stuff. Average7 is only used as a >domain for visualizing group data, although you are better off making an >average of the subjects in your study and using it instead (in which case >you shouldn't need average7 at all) > >cheers, >Bruce > > >On Tue, 5 Apr 2005 orphoebe(a)polyu.edu.hk wrote: > >> Hi, >> >> I just found out that I forgot to link average7 when I did >> the 'recon-all' on two subjects' brain data. Will it affect >> the talairach coordinates? Do I need to do the brain >> inflation again? Also, I found that the label files, e.g. >> lh.aparc.annot and rh.aparc.annot, which are expected to be >> in the 'labels' sub-folder of the subject directory. Is >> there any way that I can generate these labels files >> again? >> >> Thank you for your help in advance. >> >> Phoebe >> >> --- >> Phoebe Suk-tak Chan, Ph.D. >> Assistant Professor >> The Hong Kong Polytechnic University >> Department of Optometry and Radiography >> Hunghom, Kowloon >> Hong Kong SAR >> Tel: (852) 2766 6095 >> Fax: (852) 2764 6051 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > --- Phoebe Suk-tak Chan, Ph.D. Assistant Professor The Hong Kong Polytechnic University Department of Optometry and Radiography Hunghom, Kowloon Hong Kong SAR Tel: (852) 2766 6095 Fax: (852) 2764 6051

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Talaraich Problems
by Calabrese Massimiliano 30 Mar '05

30 Mar '05

Thank you very much Kevin for your help! Now I have fixed my problem on Lib.glut libraries Unfortunately , I have another problem ( I hope is the lastone) If I run recon-all -stage1 the computer freezes as the following point: writing to orig/orig.mnc... Outputting Volume: ............................................................ -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm At this point, the machine needs to be rebooted because the process never finishes. The software MNI seems to be correctly installed, but maybe there is some other line to add in order to config correctly. Thanks a lot for your help Massimiliano Calabrese Neuroimmunology Branch NINDS, NIH

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Freeglut problem
by Calabrese Massimiliano 30 Mar '05

30 Mar '05

Hi all I've installed Freesurfer and when I open csurf to edit segmentation on images, I get the following error: /usr/local/freesurfer/bin/Linux/tkmedit: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory Now, I've installed Freeglut and still get the above error. I can see the libglut.so.3 library in /usr/local/lib and this is in my $PATH. Any ideas why the error exists? Thanks a lot for your help Massimiliano Calabrese Neuroimmunology Branch, NINDS, NIH and Willy Calderon NINDS, NIH.

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tkmedit problems
by Mike Angstadt 29 Mar '05

29 Mar '05

Hi, I just installed freesurfer and was trying to run tkmedit. At first it couldn't find the correct shared libraries because we have 8.4 of TCL and TK installed, so I made symbollic links to those to satisfy the dependency, and it at least gets through that check. However, now when I try to run it remotely or on the local computer I get first the following: Xlib: connection to ":0.0" refused by server Xlib: No protocol specified even so a window pops up for several seconds then disappears. The .xdebug_tkmedit file says: Tix_Init returned 1: version conflict for package "Tcl": have 8.4, need 8.3 ERROR: Initializing Tix Error initializing Tix So obviously it's still having a problem with the newer versions of Tcl. Does anyone have an idea of how to fix this without uninstalling the newer Tcl/Tk? Incidentially tksurfer works fine. Thanks -Mike

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flattening
by Ronald E Bryan (rbryan＠Princeton.EDU) 26 Mar '05

26 Mar '05

Hi We are trying to create flattened surfaces for doing surface based statistical analysis of ventral temporal cortex, but the flattening method described in the freesurfer manual creates cuts right through this region. It would be better for us if we had a contiguous region of VT cortex to analyse. Are there any other slicing methods known that produce good flat maps without going through VT? thanks, -Ronnie

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Re: [Freesurfer] new tcl and tk
by xmeadow＠uchicago.edu 24 Mar '05

24 Mar '05

Hi, I saw that this question has been asked a few time with no response so I've started working on a workaround. So far, I've tried creating symoblic links from libtkx8.3.so to libtk8.3.so and the same with libtclx8.3.so. When I do this and try to view a volume it opens and the title bar is set but then crashes, before an image actually comes up, with the following error: /opt/freesurfer_alpha/bin/Linux/tkmedit bert T1 -csurf /opt/freesurfer_alpha/bin/Linux/tkmedit: symbol lookup error: /opt/freesurfer_alpha/bin/Linux/tkmedit: undefined symbol: Tcl_CreateInterp Does anyone know what this error means or a way to fix it? I'll keep working on this and post anything that works, but any help would be greatly appreciated. Thanks so much. -Xander ---- Original message ---- >Date: Tue, 22 Mar 2005 14:36:02 -0600 >From: Xander Meadow <xmeadow(a)uchicago.edu> >Subject: [Freesurfer] new tcl and tk >To: free surfer <freesurfer(a)nmr.mgh.harvard.edu> > >Hi, > >I'm running Freesurfer on RedHat Enterprise linux stations and we >recently updated to version 4 of RedHat. Doing that updated our libtcl >and libtk libraries to libtcl8.4.so and libtk8.4.so. Our problem arises >because freesurfer is still looking for version 8.3 of both libraries. >Is there a settings file where I can make this change? Or, am I behind >in my version of freesurfer? I thought I'd stayed up to date, but I >could easily be mistaken. Thanks so much. > > >-Xander > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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