Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

auto segmentation editing
by David Soscia 23 Aug '05

23 Aug '05

Guys, If you run the auto segmentation editor in the new program, does it do the defect editing (optical nerve, fornix, lateral ventricle, basal ganglia) for you, eliminating the time it takes to do this? If this is true, it is a life (and time) saver for me. Dave David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad(a)mail.amc.edu

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Stage 1 Problem
by Daniel Goldman 22 Aug '05

22 Aug '05

Hello, When I try running the stage one portion of the recon-all script on one of my subjects, the skull-stripping removes everything above the ears and everything but the skull below the ears. When I run mri_watershed, it works just fine. Any idea what I might have done wrong in running the stage one portion to have caused this? - Daniel #----------------# Daniel Goldman CENAGN @ MGH-NMR #----------------#

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Fw: Re: [Freesurfer] coregistration
by antao＠itsa.ucsf.edu 22 Aug '05

22 Aug '05

I have a image xAD1378-T1.img with spm format. after I converted it to COR with mri_convert xAD1378-T1.img AD1378/mri/orig and run FLIRT as Xiao suggests, I found that the anterior and posterior parts of tranformed image was inversed. Xiao thinks it is due to mri_convert, Does anyone know how to fix it? thx, Antao ---------- Forwarded message ---------- From: Xiao Han <xhan(a)nmr.mgh.harvard.edu> Date: Mon, 22 Aug 2005 16:03:46 -0400 (EDT) Subject: Re: [Freesurfer] coregistration It has nothing to do with fsl_register. It's because of the conversion from .img to COR format. That's why I suggested you to convert all your data to COR or mgz first before processing. The reason is because Analyze store data in an anterior-to-posterior fashion, but when mri_convert read the data, it assumed posterior-to-anterior (due to a missing .mat file). I dont know how to fix that. You can send an email to freesurfer list. -Xiao On Mon, 22 Aug 2005, antao(a)itsa.ucsf.edu wrote: > After I run: > fsl_register_new -i AD1378/mri/orig -r average_305.mnc -o AD1378/tmp/orig > -dof 9 -cost corratio -ltamat AD1378/mri/transforms/talairach.lta > > I check the tranformation with: tkmedit -f average_305.mnc -aux > AD1378/tmp/orig. I find that the anterior and posterior parts of the > image AD1378/tmp/orig are inversed. Do you know why? > > When I run fsl_register_new with images .img before converting to COR, > the result was good. > > Antao > > n Mon, 22 Aug 2005 14:16:34 -0400 (EDT) Xiao Han wrote: > >> On Mon, 22 Aug 2005, antao(a)itsa.ucsf.edu wrote: >> >>> This are the steps I use fsl_register_new: >>> 1) mksubjdir AD1378 >>> 2) mri_convert xAD1378-T1.img AD1378/mri/orig >>> 3) fsl_register_new -i AD1378/mri/orig -r average_305.mnc -o >>> AD1378/mri/orig -dof 9 -cost corratio -ltamat >>> AD1378/mri/transforms/talairach.lta >>> >>> I have a question here. Should I replace orig when I run >> fsl_register_new >>> or I should choose different filename? >> >> No, you shouldn't replace the original orig. Use a different name for the >> -o option. >> >>> After I run fsl_register_new, I should replace talairach.xfm in >> recon-all >>> script to talairach.lta and run recon-all. Do I need add -notalairach in >>> stage1? >> >> Right, you can replace talariach.xfm with talairach.lta. Also specify >> -notalairach when you run recon-all. >> >> -Xiao >> > > > >

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Tiger and MNI Linear Register
by Yuan-Fen Kuo 22 Aug '05

22 Aug '05

Hi. I have installed the freesurfer-Darwin-tiger-full.dmg and I would like to use the MNI Linear Register option. I have been prompted that "MNI has not been align not yet implemented." Because of this message, I have changed my SetUpFreeSurfer.csh script so that the following directories are pointed to the corresponding path instead of the default that came with the package. MINC_BIN_DIR /Users/Shared/freesurfer/lib/mni/bin MINC_LIB_DIR /Users/Shared/freesurfer/lib/mni/lib PERL5LIB /System/Library/Perl/5.8.6 However, I still get the same message. Is there something I am missing? Thanks in advance. Eric

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Re: [Freesurfer] process volume again
by David Soscia 22 Aug '05

22 Aug '05

Thanks, after a little tweaking, I managed to get part of the process going. A few things I thought I would mention though... 1. At first when I tried to do the -nuintensitycor command it was saying it found no data in /mri (no orig.mgz file there). When I did mksubjdirs, it made folders for all of the steps (orig, T1, wm, brain, etc) And then when I did a conversion to mgz from dicom of my orig files, they went into my orig folder, ie. mri/orig/orig.mgz. Maybe I did the conversion wrong so it sent it there instead of in the mri directory, however I thought the purpose of the mksibjdirs was to make seperate folders to put the seperate steps into. After I saw this error message in the -nuintensitycor process, I moved the orig.mgz file from the orig directory into the mri directory and it worked fine. 2. When I run the next step, -normalization, I am getting an error half way through... [amc@amcpacs 1768-4]$ recon-all -subjid 1768-4 -normalization -mgz INFO: SUBJECTS_DIR is /home/amc/freesurfer_new/freesurfer/subjects ######################################## program versions used $Id: recon-all-nmr,v 1.72 2005/07/12 15:56:32 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 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 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using mgz format --------------------------------------------- Intensity Normalization Mon Aug 22 09:14:14 EDT 2005 /home/amc/freesurfer_new/freesurfer/subjects/1768-4/mri mri_normalize orig.mgz T1.mgz reading from orig.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 Segmentation fault ERROR: mri_normalize exited with non-zero status recon-all exited with errors at Mon Aug 22 09:15:16 EDT 2005 Any ideas on what the problems could be? Thanks for your help so far. Dave David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad(a)mail.amc.edu >>> "Brian T. Quinn" <btquinn(a)nmr.mgh.harvard.edu> 08/20/05 3:49 PM >>> hi Dave- it sounds like you may be skipping some steps. what volume do you currently have? the order of the volumes to be created is: orig->nu->T1->brain->wm the -segmentation step only runs the brain->wm step. if you have an orig volume, use either: -stage1 or: -nuintensitycor -normalization -usenuintensitycor -skullstrip -segmentation stage one will take you a bit further down the FS stream, but will produce the wm volume. as for the -COR and -mgz flags, use whatever is appropriate. thanks, brian t. quinn On Fri, 19 Aug 2005, David Soscia wrote: > hey guys, > > Now I am getting this error when trying to process the volume: > > [amc@amcpacs 1768-4]$ recon-all -subjid 1768-4 -mgz -segmentation > INFO: SUBJECTS_DIR is /home/amc/freesurfer_new/freesurfer/subjects > ######################################## > program versions used > $Id: recon-all-nmr,v 1.72 2005/07/12 15:56:32 greve Exp $ > $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ > mri_convert --version > $ > $Header: > /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 > 1999/10/19 14:45:31 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 > 6.2 1999/10/19 14:45:27 neelin Exp $ > $Header: > /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 > 1999/10/19 14:45:18 neelin Exp $ > $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ > mri_convert --version > $ > # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ > # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > $ > ####################################### > Using mgz format > --------------------------------------------- > Segmentation Fri Aug 19 13:30:42 EDT 2005 > ERROR: cannot find brain.mgz > recon-all exited with errors at Fri Aug 19 13:30:42 EDT 2005 > > > i dont have a brain.mgz in the brain directory because I thought the > purpose of this process was to create it. Any suggestions? > > Dave > > David A. Soscia > Neurosciences Advanced Imaging Research Center > 47 New Scotland Ave. > Albany, NY 12208-3479 > Building S Rm. 132 > P- (518)-262-0826 > C- (518)-469-8317 > sosciad(a)mail.amc.edu > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad(a)mail.amc.edu

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Re: Welcome to the "Freesurfer" mailing list (Digest mode)
by Bosky Ravindranath 21 Aug '05

21 Aug '05

Hi, Does anybody know when the subcortical segmentation feature in Freesurfer is going to be released? Bosky

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libtk8.3.so error
by Bosky Ravindranath 21 Aug '05

21 Aug '05

I recently installed freesurfer on my Linux machine that runs RH9. When running tkmedit , I get the following error: tkmedit: error while loading shared libraries: libtk8.3.so: cannot open shared object file: No such file or directory I tried a solution posted to a simliar problem by downloading the lib files, but I got this message: rpm -i {tcl,tk}-8.3.2-1.i386.rpm package tcl-8.3.5-88 (which is newer than tcl-8.3.2-1) is already installed How do I get rid of this problem? Also, is the subcortical segmentation feature released in freesurfer-Linux-rh9-dev20050729.tar.gz? Regards, BR

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process volume again
by David Soscia 20 Aug '05

20 Aug '05

hey guys, Now I am getting this error when trying to process the volume: [amc@amcpacs 1768-4]$ recon-all -subjid 1768-4 -mgz -segmentation INFO: SUBJECTS_DIR is /home/amc/freesurfer_new/freesurfer/subjects ######################################## program versions used $Id: recon-all-nmr,v 1.72 2005/07/12 15:56:32 greve Exp $ $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $ mri_convert --version $ $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 1999/10/19 14:45:31 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 6.2 1999/10/19 14:45:27 neelin Exp $ $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 1999/10/19 14:45:18 neelin Exp $ $Id: talairach2,v 1.7 2004/08/31 18:07:37 tosa Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $ # $Id: nu_estimate.in,v 1.15 1999/08/10 18:05:42 jgsled Exp $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### Using mgz format --------------------------------------------- Segmentation Fri Aug 19 13:30:42 EDT 2005 ERROR: cannot find brain.mgz recon-all exited with errors at Fri Aug 19 13:30:42 EDT 2005 i dont have a brain.mgz in the brain directory because I thought the purpose of this process was to create it. Any suggestions? Dave David A. Soscia Neurosciences Advanced Imaging Research Center 47 New Scotland Ave. Albany, NY 12208-3479 Building S Rm. 132 P- (518)-262-0826 C- (518)-469-8317 sosciad(a)mail.amc.edu

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Fwd: Re: [Freesurfer] mri_watershed
by Sasha Wolosin 19 Aug '05

19 Aug '05

Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270

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mri_watershed
by Sasha Wolosin 19 Aug '05

19 Aug '05

We use an anatomical analysis program called Brain Image in our lab. We would like to speed up our analysis in Brain Image by replacing manual skull stripping with FreeSurfer's automated skull strip program. For this we would need to do a skull strip alone, without adjusting intensity values or contrast. Is this possible? Is this a reasonable thing to do? I have run mri_watershed with the input from orig on several subjects, and the output volume looks much brighter than the orig volume. Does mri_watershed normalize intensities or change the contrast in order to strip the skull? 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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Freesurfer