Freesurfer October 2004

freesurfer@nmr.mgh.harvard.edu

27 participants
37 discussions

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

2 1

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

1 0

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

3 2

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 >

3 2

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

2 1

(no subject)
by Joongnam Yang 19 Oct '04

19 Oct '04

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 --------------------------

2 1

mri_montion_correct2 utility
by Kushal Koolwal 19 Oct '04

19 Oct '04

hi everyone, Well I couldn't run the mri_motion_correct on my Mac machine but I found another tool called mri_motion_convert2 in the /bin/noarch folder of freesurfer. I was able to run the utility by specifying output directory and the input files. But after it did all the processing it gives an error like: Motion Correcting /tmp/cor-2.mnc Mon Oct 18 15:03:59 PDT 2004 Error: opening MINC file "/tmp/cor-2.mnc". Error in minctracc in file minctracc.c, line 381 Cannot input volume '/tmp/cor-2.mnc'ERROR: mritoself failed [d99-94:bert/mri/orig] scottfre% I am attaching the error log file if any one wants to have a detail look. Sincerely, Kushal Koolwal _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com

5 5

mri_montion_correct command not found on Mac OS X
by Kushal Koolwal 19 Oct '04

19 Oct '04

hi, I am using MAC OS X and when i try to run the mri_motion_correct command it says that this command should be run on a linux machine. DoI have to use the register.csh command that they have specified in the manual. I even did that once but I got errors in between the process. this is the output that I get when I try to run mri_montion-convert. [d99-94:bert/mri/orig] scottfre% ls 001 002 003 [d99-94:bert/mri/orig] scottfre% mri_motion_correct . 001 002 003 mri_motion_correct must be run on a Linux machine thanks. Kushal _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com

3 3

Freesurfer download site
by Kristine Beate Walhovd 19 Oct '04

19 Oct '04

Hi I was just going to download Freesurfer again. However, the Freesurfer site I have used previously seem sto be down: http://surfer.nmr.mgh.harvard.edu Do I have the wrong address? I'd be grateful for directions on where to find the latest version now. Thanks, Kristine

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Freesurfer October 2004