[Freesurfer] tkregister2
Dear all, I am having trouble running tkregister2. I get an error when I run tkregister2 on a subject after running autorecon1 (see below.) However, I also get an error when I run it on bert. It seems tkregister2 is searching for COR files, but I am using mgz format. Am I not using the correct flags? My subjects directory contains the talairach subject included in the dev release. Do I need to download talairach separately? Here is the output for subject 2335 and bert: [EMAIL PROTECTED] talairach]$ tkregister2 --mgz --s 2335 --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm - 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 [EMAIL PROTECTED] subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm - 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 [EMAIL PROTECTED] subjects]$ Any help is greatly appreciated. Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2
I just fixed this error. For those in the nmr center, the fix will be live tomorrow. For those outside, you can download a new Linux version from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ Sasha Wolosin wrote: Dear all, I am having trouble running tkregister2. I get an error when I run tkregister2 on a subject after running autorecon1 (see below.) However, I also get an error when I run it on bert. It seems tkregister2 is searching for COR files, but I am using mgz format. Am I not using the correct flags? My subjects directory contains the talairach subject included in the dev release. Do I need to download talairach separately? Here is the output for subject 2335 and bert: [EMAIL PROTECTED] talairach]$ tkregister2 --mgz --s 2335 --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm - 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 [EMAIL PROTECTED] subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm - 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 [EMAIL PROTECTED] subjects]$ Any help is greatly appreciated. Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkregister2
Sasha, An alternative solution is to create the COR files for the talairach subject: cd $SUBJECTS_DIR/talairach/mri mri_convert -it mgz -ot cor orig.mgz orig/ This will deposit COR files into the orig/ directory, and your current tkregister2 should then work. We are recommending using .mgz files over the older COR format, and are still trying to make all the tools fully compliant. A new 'dev' release containing the updated tkregister2 will be posted in the next couple days. Nick On Thu, 2005-09-15 at 14:26 -0400, Doug Greve wrote: > I just fixed this error. For those in the nmr center, the fix will be > live tomorrow. For those outside, you can download a new Linux version > from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > Sasha Wolosin wrote: > > >Dear all, > > > > I am having trouble running tkregister2. > > > > I get an error when I run tkregister2 on a subject after running > > autorecon1 (see below.) However, I also get an error when I run it on > > bert. > > It seems tkregister2 is searching for COR files, but I am using mgz > > format. Am I not using the correct flags? > > > > My subjects directory contains the talairach subject included in the dev > > release. Do I need to download talairach separately? > > > >Here is the output for subject 2335 and bert: > >[EMAIL PROTECTED] talairach]$ tkregister2 --mgz --s 2335 --fstal > >INFO: no target volume specified, assuming FreeSurfer orig volume. > >target volume orig > >movable volume (null) > >reg file (null) > >LoadVol1 > >$Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ > >Diagnostic Level -1 > >talairach.xfm - > > 1.002 0.050 -0.017 -3.539; > >-0.053 1.034 -0.076 -12.275; > > 0.014 0.081 1.091 -14.424; > > 0.000 0.000 0.000 1.000; > >corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info > >ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 > > > > > >[EMAIL PROTECTED] subjects]$ tkregister2 --mgz --s bert --fstal > >INFO: no target volume specified, assuming FreeSurfer orig volume. > >target volume orig > >movable volume (null) > >reg file (null) > >LoadVol1 > >$Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ > >Diagnostic Level -1 > >talairach.xfm - > > 1.154 -0.024 0.046 -5.813; > > 0.014 0.941 0.131 -21.893; > >-0.048 -0.155 1.123 -0.730; > > 0.000 0.000 0.000 1.000; > >WARNING: can't find the talairach xform > >'/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm' > >WARNING: transform is not loaded into mri > >corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info > >ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 > >[EMAIL PROTECTED] subjects]$ > > > > > >Any help is greatly appreciated. > > > >Thanks, > >Sasha > > > > > >Sasha Wolosin > >Research Assistant > >Developmental Cognitive Neurology > >Kennedy Krieger Institute > >707 N. Broadway > >Baltimore, MD 21205 > >ph: (443) 923-9270 > >[EMAIL PROTECTED] > > > > > > > >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. > > > >___ > >Freesurfer mailing list > >Freesurfer@nmr.mgh.harvard.edu > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] average curvatures
Hello, I am trying to superimpose an average curvature on the inflated brain surface of another subject. I know that you can use mris_average_curvature to create an average curvature of some specified brains, but I would like to use an average curvature that is not an average of the subjects' curvatures; instead, I'd like it to be an average of curvatures from a general atlas. How do I create, based on this average, the lh.avg_curv and rh.avg_curv files in a subject's surf/ directory? Thanks, Sheeva Azma ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] average curvatures
Hi Sheeva, you can use mrisp_paint: mrisp_paint $FREESURFER_HOME/average/lh.average.tif#6 \ $SUBJECTS_DIR/$subject/surf/lh.sphere.reg \ $SUBJECTS_DIR/$subject/surf/lh.avg_sulc mrisp_paint $FREESURFER_HOME/average/lh.average.tif#3 \ $SUBJECTS_DIR/$subject/surf/lh.sphere.reg \ $SUBJECTS_DIR/$subject/surf/lh.avg_curv cheers, Bruce On Thu, 15 Sep 2005, Sheeva Azma wrote: Hello, I am trying to superimpose an average curvature on the inflated brain surface of another subject. I know that you can use mris_average_curvature to create an average curvature of some specified brains, but I would like to use an average curvature that is not an average of the subjects' curvatures; instead, I'd like it to be an average of curvatures from a general atlas. How do I create, based on this average, the lh.avg_curv and rh.avg_curv files in a subject's surf/ directory? Thanks, Sheeva Azma ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] intensity normalization failure
Hi, Just had a couple of questions re: the -pvvol flag in mri_segstats: How does it take account of partial voluming? Is there anyway to visualize what the partial volume-corrected volume would look like? Would you recmmoned using this falg routinely to obtain subcortical volumes? Finally, on a completely unrelated question, is there any reason to think that surfaces created using the same freesurfer distribution on a Mac would be incompatible with those created using a Linux machine (ie., would you be able to pool them for one study without any problems, and could you start creating surfaces on one, and then re-run afdter manual edits on the other?) Thanks, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 9/15/2005 10:11 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu; Tracy Wang Subject:RE: [Freesurfer] intensity normalization failure You should be able to use mri_segstats somehow. You'll need a segmentation, though. You could tell it to report on the aseg wm values. You could also use the fill volume (127 and 255?). Check out the --help doug On Wed, 14 Sep 2005, Bruce Fischl wrote: > should be easy enough to do in matlab. Just load the wm volume, then find all > the T1 voxels that are nonzero in it. > > Bruce > On Thu, 15 Sep 2005, Fornito, Alexander wrote: > >> Is it possible to obtain and intensity histogram of the wm voxels, or >> descriptive stats (eg., Mean, SD) as a quick check? >> >> -Original Message- >> From: Bruce Fischl [mailto:[EMAIL PROTECTED] >> Sent: Thursday, September 15, 2005 3:33 AM >> To: Tracy Wang >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] intensity normalization failure >> >> if it succeeds then the intensity in the wm should be exactly 110 over >> much of the brain, and 90> >> Bruce >> >> On Wed, 14 Sep >> 2005, Tracy Wang wrote: >> >>> Hi >>> >>> What is a typical example of when the intensity normalization process >> fails? >>> Does the over-all image seem brighter? What is a good indicator of >> success >>> or failure? >>> >>> Thanks, >>> Tracy >>> >>> >>> Tracy Wang >>> Research Assistant >>> Cognitive Neuroscience Laboratory >>> >>> Washington University >>> Department of Psychology, Campus Box 1125 >>> One Brookings Drive >>> St. Louis MO 63130-4899 >>> 314-935-5019 >>> [EMAIL PROTECTED] >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] intensity normalization failure
Hi Alex, the -pvol flag assumes ever border voxel is a linear combination of the class that it is labeled as and another class that it borders. The local class means are computed by as the sample mean in a local window of all non border voxels of that class. The mac and linux version should be compatible, as long as you make sure they are the same version of the software. cheers, Bruce On Fri, 16 Sep 2005, Fornito, Alexander wrote: Hi, Just had a couple of questions re: the -pvvol flag in mri_segstats: How does it take account of partial voluming? Is there anyway to visualize what the partial volume-corrected volume would look like? Would you recmmoned using this falg routinely to obtain subcortical volumes? Finally, on a completely unrelated question, is there any reason to think that surfaces created using the same freesurfer distribution on a Mac would be incompatible with those created using a Linux machine (ie., would you be able to pool them for one study without any problems, and could you start creating surfaces on one, and then re-run afdter manual edits on the other?) Thanks, Alex -Original Message- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Thu 9/15/2005 10:11 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu; Tracy Wang Subject:RE: [Freesurfer] intensity normalization failure You should be able to use mri_segstats somehow. You'll need a segmentation, though. You could tell it to report on the aseg wm values. You could also use the fill volume (127 and 255?). Check out the --help doug On Wed, 14 Sep 2005, Bruce Fischl wrote: should be easy enough to do in matlab. Just load the wm volume, then find all the T1 voxels that are nonzero in it. Bruce On Thu, 15 Sep 2005, Fornito, Alexander wrote: Is it possible to obtain and intensity histogram of the wm voxels, or descriptive stats (eg., Mean, SD) as a quick check? -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Thursday, September 15, 2005 3:33 AM To: Tracy Wang Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] intensity normalization failure if it succeeds then the intensity in the wm should be exactly 110 over much of the brain, and 90 Hi What is a typical example of when the intensity normalization process fails? Does the over-all image seem brighter? What is a good indicator of success or failure? Thanks, Tracy Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
