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MNI auto talairaching
by Wan Park 29 Oct '04

29 Oct '04

could you please tell me how to do auto talairaching with the MINC? thanks wan

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tkregister2 question
by George Papadimitriou 27 Oct '04

27 Oct '04

I am trying to register a lowb volume to an average volume. In this particular case, I'm trying to use tkregister2: % tkregister2 --targ avg_000.bfloat --mov indivsubj_000.bfloat --reg \ register.dat I am having a problem with the brightness of the TARG volume. It seems to be set near ~1, and using the fmov option only adjusts the brightness on the MOV volume. It is kind of hard to align them, when the target volume looks like a binary mask (appears all white). Have you seen this before? Changing the contrast doesn't seem to help. Thanks, George P.

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when I am creating the surface
by Wan Park 26 Oct '04

26 Oct '04

I start with the filling of white matter but after a while I am receiving this massage: (...) using +/- offset search region where offset is 45..... using +/- offset search region where offset is 48..... /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_fill: could not find pons No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (2.00, 29.00, -8.00) INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... Command Finished could you help me with this? thanks, wan park

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segmentation fault during fill step
by Jason 25 Oct '04

25 Oct '04

The white matter surface creation step resulted in a poor L/R hemisphere separation in one of my subjects. A portion of the cut is shifted into the left hemisphere white matter (running from the corpus callosum downward to the brain stem). To remedy this I ran the following command to manually set the corpus callosum cutting planes: recon-all -subjid pbb_subj.07 -fill -cc-xyz 131 125 146 I encountered the following error: Searching for cutting planes.Segmentation fault (core dumped). Can you offer me any advice on how to remedy this problem? Thanks, Jason

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angled cutting planes/pons removal
by Nguyen, Thang Q 25 Oct '04

25 Oct '04

Hi all, I have a few subjects who have angled cutting planes. I ran talairach <subjid> and rerun the mri_fill and there is a very angled cut. A reason for this may be that the pons have been removed during white matter segmentation. The brain images have the pons intact but the wm images don't. I've run recon-all stage1, segment_subject, and process volume from the csurf interface. They all remove the pons. I've also tracked the coordinates of the pons in the brain volumes and used those in the mri_fill command (-P <x> <y> <z>). Is there a reason for this and a way to fix it? Thank you, Thang Nguyen

4 3

Missing MNI coordinates
by Kristine Beate Walhovd 21 Oct '04

21 Oct '04

Hi I just discovered that I'm lacking the MNI coordinates in Freesurfer2004-02-18. I just updated this version with the new mri_convert and mri_watershed fix (putting these in the freesurfer/bin/Linux directory). That couldn't create this problem? Any suggestions appreciated. Thanks, Kristine

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problems with mritotal on OSX
by Emmette Hutchison 20 Oct '04

20 Oct '04

Hi all, I have encountered a few errors that seem to be caused by mritotal when creating the talairach.xfm file. I've attached environment information and the error output below. I'm running FreeSurfer (20040218) on OSX 10.3 using the MNI tools provided with the FreeSurfer distribution. (mritotal is v 1.11.2.1 2003/11/17.) I'm also using perl v5.8.1-RC3. Has anyone encountered this problem and is there a solution? Thanks, Emmette ________________________________________________ talairach aVOTD registering aVOTD mri_convert orig orig/orig.mnc reading from orig... TR=1.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... Variable "$ProgramName" is not imported at freesurfer/minc/bin/mritotal line 210. Variable "$ProgramName" is not imported at freesurfer/minc/bin/mritotal line 210. Variable "$ProgramName" is not imported at freesurfer/minc/bin/mritotal line 210. Variable "$ProgramName" is not imported at freesurfer/minc/bin/mritotal line 217. Variable "$ProgramName" is not imported at freesurfer/minc/bin/mritotal line 217. Variable "$ProgramName" is not imported at freesurfer/minc/bin/mritotal line 217. Variable "$ProgramName" is not imported at freesurfer/minc/bin/mritotal line 265. Variable "$ProgramName" is not imported at freesurfer/minc/bin/mritotal line 422. Global symbol "$Clobber" requires explicit package name at freesurfer/minc/bin/mritotal line 108. Global symbol "$TmpDir" requires explicit package name at freesurfer/minc/bin/mritotal line 121. Global symbol "$ProgramName" requires explicit package name at freesurfer/minc/bin/mritotal line 210. Global symbol "$ProgramName" requires explicit package name at freesurfer/minc/bin/mritotal line 210. Global symbol "$ProgramName" requires explicit package name at freesurfer/minc/bin/mritotal line 210. Global symbol "$ProgramName" requires explicit package name at freesurfer/minc/bin/mritotal line 217. Global symbol "$ProgramName" requires explicit package name at freesurfer/minc/bin/mritotal line 217. Global symbol "$ProgramName" requires explicit package name at freesurfer/minc/bin/mritotal line 217. Global symbol "$ProgramName" requires explicit package name at freesurfer/minc/bin/mritotal line 265. Global symbol "@DefaultArgs" requires explicit package name at freesurfer/minc/bin/mritotal line 281. Global symbol "$ProgramName" requires explicit package name at freesurfer/minc/bin/mritotal line 422. BEGIN not safe after errors--compilation aborted at freesurfer/minc/bin/mritotal line 455. Error: could not open file "/bsp/speechlab/users/emmette/FreeSurfer//aVOTD/mri/transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file 'FreeSurfer//aVOTD/mri/transforms/talairach.xfm' No such file or directory

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MINC tools for Mac OS X
by Kushal Koolwal 20 Oct '04

20 Oct '04

hi, Well I am running into some serious problems while running csurf on my Mac machine.... Can someone suggest a good source where I can download the MIN/MINC tools that are required for running csurf. I mean I want to use the mri_montion_correct utility as mentioned in the Freesurfer tutorial. Can someone suggest a good source for downloading the MINC tools which are required for the above purpose.? thanks, Kushal _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com

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Re: [Freesurfer] (no subject)
by Joongnam Yang 19 Oct '04

19 Oct '04

Hi Bruce, I've checked the system and found the MNI package is installed. (Someone installed it a while ago) When I did "locate nu_correct" for the error message, there was nothing on "nu_correct". There was a huge directory that includes MNI stuff. So, it is installed but there is NO such thing as "nu_correct". What would you recommend me to do next? (1) Install it again, or (2) I don't have to do it, since the error message is only due to mistakes in one of the environment variables for MNI package. If so, is there any source for correcting environment variables for the MNI package? Nam. >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 10/19/04 3:16 PM >>> it looks like you don't have the MNI software installed (nu_correct comes from there) Bruce On Tue, 19 Oct 2004, Joongnam Yang wrote: > Hi, > > I used the following command > > recon-all -stage1 -subjid blobby > > and I got the following error message > (Please let me know what is wrong with Freesurfer). > > -------------- copy of the exact error messages ------------------- > ######################################## > program versions used > $Id: recon-all-nmr,v 1.37 2004/01/06 22:21:48 tosa Exp $ > $Id: mri_motion_correct2,v 1.7 2004/01/16 20:25:10 tosa Exp $ > mri_convert --version > $ > $Header: /software/source//minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v > 6.8 2002/08/05 00:53:50 neelin Exp $ > minctracc.c > $Header: > /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v > 96.3 2000/03/15 08:42:41 stever Exp $ > $Header: > /software/source//minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.11 > 2002/11/06 13:32:23 jason Exp $ > $Header: > /software/source//minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.4 > 2001/04/24 13:38:42 neelin Exp $ > $Id: talairach2,v 1.5 2003/08/28 21:45:48 tosa Exp $ > mri_convert --version > $ > # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ > strings: nu_correct:: No such file or directory > strings: Command: No such file or directory > strings: not: No such file or directory > strings: found.: No such file or directory > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > ####################################### > INFO: SUBJECTS_DIR is /home/nam > ERROR: nu_correct does not exist > --------- end of the copy of the error messages -------------------------- > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Label and overlay
by Calabrese, Massimiliano (NIH/NINDS) 19 Oct '04

19 Oct '04

I'm very sorry for the stupid question: Which the functions of the labels and overlay, which the goal? Give me an example please Max

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