Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30129 discussions

Re: [Freesurfer] Tiger and MNI Linear Register
by Nick Schmansky 24 Aug '05

24 Aug '05

Eric, Hi. The MNI Linear Register option is code that is found in the MINC toolkit, and it is that code that is generating the message about not being implemented. So I am afraid you are out of luck in that respect, in that we do not maintain the MINC toolkit. I think our default registration tools do a good job though. Also, we advocate usage of the command-line tools over csurf, which is a gui that we no longer support. The reason is that it is easier to perform a work-flow from the command-line, and more importantly, it is easier to copy-and-paste any error messages that may appear in a failed run. You should have a look at the script recon-all. Type: recon-all --help This will talk about the processing stages, and is the main 'front-end' to the freesurfer tools. We will be releasing an online tutorial soon that will fully describe a workflow using recon-all. Per the message about perl found in your email, freesurfer does use the perl executable installed on the machine, and the MNI tools puts there perl scripts in the path found in the PERL5LIB that freesurfer prints out. That path looks like the /System path I think only because it makes clear which perl version MNI is using. Nick On Wed, 2005-08-24 at 14:45 -0500, Yuan-Fen Kuo wrote: > Hi Nick: > Thanks for your reply and sorry for my late reply. > > I have checked the "MNI Linear Register" option in the expert > Preference. > When I run "Convert/Average" in "Setup Structural Scan > Parameters" I am prompted with the following message "MNI align not > yet implemented." in a popped up window. I do all these in the GUI. > I did check the log window, and no messages were printed out in > there. I have installed the full package ( freesurfer-Darwin-tiger- > full.dmg ) with no customization. > > In the previous message I have mentioned my changes to the > SetUpFreeSurfer.csh script. I have figured out why I did not need to > make the modificaitons, however, if you are still interested, I do > explain why I made the changes below. > > > Thank you, > Eric > > ********************************* > > > > > 1) I used to un-comment the following lines in > SetUpFreeSurfer.csh attempting to use the MINC tools ( as modifying > the script is usually the first step any tutorial instructs. ) > > #setenv MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin > #setenv MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib > > I realized that these directories do not exist so I changed them to > > MINC_BIN_DIR /Users/Shared/freesurfer/lib/mni/bin > MINC_LIB_DIR /Users/Shared/freesurfer/lib/mni/lib > > then I finally realized that if I do not un-comment the two > lines in SetUpFreesurfer.csh, the two variables will anyway be set to > > MINC_BIN_DIR /Users/Shared/freesurfer/lib/mni/bin > MINC_LIB_DIR /Users/Shared/freesurfer/lib/mni/lib > > so I have no problem with these two variables now. However, > perhaps it should be modified in the > SetUpFreeSurfer.csh script to avoid confusion? > > > 2) PERL5LIB is set to > > /Users/Shared/freesurfer/lib/mni/lib/../System/Library/Perl/5.8.6 > > while this package is a tiger package, perhaps we can use the > Perl that comes with Tiger in > > /System/Library/Perl/5.8.6 > > I realize in FreeSurferEnv.csh, Tiger's Perl is checked, but it > is nevertheless set back to > > /Users/Shared/freesurfer/lib/mni/lib/../System/Library/Perl/5.8.6 > > > > > On Aug 22, 2005, at 3:39 PM, Nick Schmansky wrote: > > > Yuan-Fen, > > > > Hello, I think I need more information before I can diagnose the > > problem. What is being run when the error message appears? If you > > could copy and paste the command-line output, that would be helpful. > > > > Also, I am not sure what was changed in the SetUpFreeSurfer.csh > > script, > > as the MINC_BIN_DIR and MINC_LIB_DIR vars are correct (and are the > > default). What were they set to prior? > > > > Thanks, > > > > Nick > > > > > > On Mon, 2005-08-22 at 14:50 -0500, Yuan-Fen Kuo wrote: > > > >> 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 > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >

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paradigm ill-conditioned
by Hans Op de Beeck 24 Aug '05

24 Aug '05

Hi all, When I run selxavg-sess, I sometimes get the following error message at the beginning of the algorithm (right after I get the Residual Error Estimation): ERROR: paradigm is ill-conditioned (1.17293e+07) Check your paradigm file for file for periodicities My paradigm is fairly simple. It is a block-design, I use -gammafit, and there are 3 conditions that I present in 3 different orders across runs (e.g., in one run it might be 0 1 2 3 0 3 2 1 0). I always use the same paradigm-files, and this error message doesn't appear always. In general I include the motion-correction parameters as covariates (flag -mcextreg in mkanalysis-sess.new). The problem is easily solved by not including the motion-correction parameters in the analysis. Can this error message be caused by a strong correlation between 2 of my mc-parameters ? What is the best solution in that case ? Maybe to compute a lower number of principal components whenever the problem occurs ? Thank you for your help, Hans P. Op de Beeck Kanwisher lab

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Re: [Freesurfer] ERROR: nu_correct
by Nick Schmansky 24 Aug '05

24 Aug '05

Ok. Sorry about the hassle. On Wed, 2005-08-24 at 12:34 -0400, Keyma Prince wrote: > Ok it look good now > > thanks > > Keyma Prince > Massachusetts Institute of Technology > Department of Brain and Cognitive Sciences > NE20-392 > Cambridge, MA 02139 > > On Wed, 24 Aug 2005, Nick Schmansky wrote: > > > Ok, how about now? > > > > > > On Wed, 2005-08-24 at 12:10 -0400, Keyma Prince wrote: > > > I get the same error. > > > > > > Here is output you asked for: > > > > > > [miracle:STRUCS] (nmr-std-env) cat /etc/redhat-release > > > CentOS release 4.1 (Final) > > > [miracle:STRUCS] (nmr-std-env) uname -a > > > Linux miracle 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 > > > athlon i386 GNU/Linux > > > [miracle:STRUCS] (nmr-std-env) > > > > > > > > > Keyma Prince > > > Massachusetts Institute of Technology > > > Department of Brain and Cognitive Sciences > > > NE20-392 > > > Cambridge, MA 02139 > > > > > > On Wed, 24 Aug 2005, Nick Schmansky wrote: > > > > > > > Kayma, > > > > > > > > Can you give it a try now? > > > > > > > > Also, can you type the following for me? > > > > > > > > cat /etc/redhat-release > > > > uname -a > > > > > > > > This will tell me the machine OS and type. Unfortunately, I can't login > > > > to miracle. > > > > > > > > Nick > > > > > > > > > > > > On Wed, 2005-08-24 at 11:40 -0400, Keyma Prince wrote: > > > > > this is on miracle. I opened a new terminal window and here is the output > > > > > from nu_correct > > > > > > > > > > [miracle:STRUCS] (nmr-std-env) nu_correct > > > > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > > > > /usr/lib/perl5/5.8.5/i386-li nux-thread-multi /usr/lib/perl5/5.8.5 > > > > > /usr/lib/perl5/site_perl/5.8.5/i386-linux- thread-multi > > > > > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/per > > > > > l5/site_perl/5.8.3/i386-linux-thread-multi > > > > > /usr/lib/perl5/site_perl/5.8.2/i386-l inux-thread-multi > > > > > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/li > > > > > b/perl5/site_perl/5.8.0/i386-linux-thread-multi > > > > > /usr/lib/perl5/site_perl/5.8.5 / usr/lib/perl5/site_perl/5.8.4 > > > > > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site _perl/5.8.2 > > > > > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/l > > > > > ib/perl5/site_perl > > > > > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr > > > > > /lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > > > > > /usr/lib/perl5/vendor_perl/ 5.8.3/i386-linux-thread-multi > > > > > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread -multi > > > > > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/v > > > > > endor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 > > > > > /usr/l ib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 > > > > > /usr/lib/perl5/vendo r_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 > > > > > /usr/lib/perl5/vendor_perl/5.8.0 / usr/lib/perl5/vendor_perl .) at > > > > > /usr/pubsw/packages/mni/current/bin/nu_correct l ine 37. > > > > > BEGIN failed--compilation aborted at > > > > > /usr/pubsw/packages/mni/current/bin/nu_corr ect line 37. > > > > > > > > > > > > > > > Keyma Prince > > > > > Massachusetts Institute of Technology > > > > > Department of Brain and Cognitive Sciences > > > > > NE20-392 > > > > > Cambridge, MA 02139 > > > > > > > > > > On Wed, 24 Aug 2005, Nick Schmansky wrote: > > > > > > > > > > > Keyma, > > > > > > > > > > > > Hi, on which machine does this occur? If you start a new shell, and > > > > > > type: > > > > > > > > > > > > nu_correct > > > > > > > > > > > > What does it display? > > > > > > > > > > > > Nick > > > > > > > > > > > > > > > > > > On Wed, 2005-08-24 at 11:34 -0400, Keyma Prince wrote: > > > > > > > I just tried to run the following command and I got an error which has > > > > > > > appeared before on the freesurfer list after the MINC toolkit was rebuilt. > > > > > > > Can you let me know if this has happened again and what I can do about it? > > > > > > > > > > > > > > thanks, > > > > > > > > > > > > > > -Keyma > > > > > > > > > > > > > > > > > > > > > Command: recon-all -stage1 -subjid Y24_031905a_STRUC > > > > > > > > > > > > > > Error output: > > > > > > > > > > > > > > i_ras = (-1, 0, 0) > > > > > > > j_ras = (0, -0, -1) > > > > > > > k_ras = (-0, 1, 0) > > > > > > > Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. > > > > > > > Data is conformed to 1 mm size and 256 voxels for all directions > > > > > > > writing to .... > > > > > > > Started at: Wed Aug 24 11:21:42 EDT 2005 > > > > > > > Ended at: Wed Aug 24 11:23:46 EDT 2005 > > > > > > > mri_motion_correct2: done > > > > > > > --------------------------------------------- > > > > > > > Nu Intensity Correction Wed Aug 24 11:23:46 EDT 2005 > > > > > > > mri_convert orig nu0.mnc > > > > > > > mri_convert orig nu0.mnc > > > > > > > reading from orig... > > > > > > > TR=2530.00, TE=3.30, TI=1100.00, flip angle=7.00 > > > > > > > i_ras = (-1, 0, 0) > > > > > > > j_ras = (0, -0, -1) > > > > > > > k_ras = (-0, 1, 0) > > > > > > > writing to nu0.mnc... > > > > > > > nu_correct -clobber nu0.mnc nu1.mnc > > > > > > > Can't locate MNI/Startup.pm in @INC (@INC contains: > > > > > > > /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 > > > > > > > /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 > > > > > > > /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 > > > > > > > /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 > > > > > > > /usr/lib/perl5/site_perl > > > > > > > /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi > > > > > > > /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 > > > > > > > /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 > > > > > > > /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 > > > > > > > /usr/lib/perl5/vendor_perl .) at > > > > > > > /usr/pubsw/packages/mni/current/bin/nu_correct line 37. > > > > > > > BEGIN failed--compilation aborted at > > > > > > > /usr/pubsw/packages/mni/current/bin/nu_correct line 37. > > > > > > > ERROR: nu_correct > > > > > > > ------------------------------------------ > > > > > > > Filesystem 1K-blocks Used Available Use% Mounted on > > > > > > > engram:/local_mount/space/engram/11 > > > > > > > 68682136 44104560 24577576 65% > > > > > > > /autofs/space/engram_011 > > > > > > > ------------------------------------------ > > > > > > > recon-all exited with errors at Wed Aug 24 11:24:01 EDT 2005 > > > > > > > > > > > > > > > > > > > > > Keyma Prince > > > > > > > Massachusetts Institute of Technology > > > > > > > Department of Brain and Cognitive Sciences > > > > > > > NE20-392 > > > > > > > Cambridge, MA 02139 > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >

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ERROR: nu_correct
by Keyma Prince 24 Aug '05

24 Aug '05

I just tried to run the following command and I got an error which has appeared before on the freesurfer list after the MINC toolkit was rebuilt. Can you let me know if this has happened again and what I can do about it? thanks, -Keyma Command: recon-all -stage1 -subjid Y24_031905a_STRUC Error output: i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (-0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to .... Started at: Wed Aug 24 11:21:42 EDT 2005 Ended at: Wed Aug 24 11:23:46 EDT 2005 mri_motion_correct2: done --------------------------------------------- Nu Intensity Correction Wed Aug 24 11:23:46 EDT 2005 mri_convert orig nu0.mnc mri_convert orig nu0.mnc reading from orig... TR=2530.00, TE=3.30, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, -0, -1) k_ras = (-0, 1, 0) writing to nu0.mnc... nu_correct -clobber nu0.mnc nu1.mnc Can't locate MNI/Startup.pm in @INC (@INC contains: /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.4/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/pubsw/packages/mni/current/bin/nu_correct line 37. ERROR: nu_correct ------------------------------------------ Filesystem 1K-blocks Used Available Use% Mounted on engram:/local_mount/space/engram/11 68682136 44104560 24577576 65% /autofs/space/engram_011 ------------------------------------------ recon-all exited with errors at Wed Aug 24 11:24:01 EDT 2005 Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139

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Re: [Freesurfer] auto segmentation editing
by David Soscia 23 Aug '05

23 Aug '05

it keeps having trouble with the aseg volume: [amc@amcpacs mri]$ recon-all -subjid 1768-4 -edit_wm_with_aseg 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 $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ ####################################### ~/freesurfer_new/freesurfer/subjects/1768-4 Using mgz format --------------------------------------- Editing WM with SubCort Seg Tue Aug 23 14:01:38 EDT 2005 mri_edit_wm_with_aseg wm.mgz aseg.mgz wm.mgz zcat: /home/amc/freesurfer_new/freesurfer/subjects/1768-4/mri/aseg.mgz.gz: No such file or directory mghRead(/home/amc/freesurfer_new/freesurfer/subjects/1768-4/mri/aseg.mgz, -1): read error mri_edit_wm_with_aseg: could not read aseg volume from aseg.mgz reading wm segmentation from wm.mgz... ERROR: mri_edit_wm_with_aseg with non-zero status recon-all exited with errors at Tue Aug 23 14:01:40 EDT 2005 It cannot find any aseg.mgz volume. I dont have one, just a blank directory called aseg that was made with mksubjdirs process. I dont know where this aseg.mgz would/should have been created? 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> 08/23/05 2:08 PM >>> mri_edit_wm_with_aseg or recon-all -edit_wm_with_aseg (if it's in your version of recon-all -> grep for it.) On Tue, 23 Aug 2005, David Soscia wrote: > thats great, however when I type in the command, the computer is not > recognizing it: > > [amc@amcpacs mri]$ mri_edit_with_aseg wm aseg wm > mri_edit_with_aseg: Command not found. > > tried this way also: > > [amc@amcpacs mri]$ recon-all -subjid 1768-4 -mri_edit_with_aseg wm aseg > wm > ERROR: Flag -mri_edit_with_aseg unrecognized. > > any ideas why? > > 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 >>>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 08/23/05 1:45 PM >>> > yes, most of that (not fornix or optic nerve) > > On Tue, 23 Aug 2005, David Soscia > wrote: > >> 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 >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- brian t. quinn

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Re: [Freesurfer] auto segmentation editing
by David Soscia 23 Aug '05

23 Aug '05

thats great, however when I type in the command, the computer is not recognizing it: [amc@amcpacs mri]$ mri_edit_with_aseg wm aseg wm mri_edit_with_aseg: Command not found. tried this way also: [amc@amcpacs mri]$ recon-all -subjid 1768-4 -mri_edit_with_aseg wm aseg wm ERROR: Flag -mri_edit_with_aseg unrecognized. any ideas why? 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 >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 08/23/05 1:45 PM >>> yes, most of that (not fornix or optic nerve) On Tue, 23 Aug 2005, David Soscia wrote: > 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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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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