[Freesurfer] Vanishing Control Points
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why? -Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RE: [Freesurfer] Vanishing Control Points (Updated: MNC to MGZ problems)
Upon further investigation it seems to be something wrong with my conversion from MNC to MGZ. I have tried the exact same scan going through Analyze to MGZ and the control points work fine. Has anyone had any issues converting between mnc and mgz? -Eric -Original Message- From: Faden, Eric (NIH/NIMH) [F] Sent: Tue 8/1/2006 9:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Vanishing Control Points I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why? -Eric ___ 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] tkmedit problem
Hello- I have just installed freesurfer. Although tksurfer and tkregister2 seem to work fine, I get the following error message when attempting tkmedit: X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 15 Current serial number in output stream: 15 and I'm not sure if this helps, but when I source the SetUpFreeSurfer.csh script, I get the following: freesurfer-Darwin-tiger-stable-pub-v3.0.3 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast SUBJECTS_DIR/Applications/freesurfer/subjects FUNCTIONALS_DIR /Applications/freesurfer/sessions MINC_BIN_DIR/Applications/freesurfer/mni/bin MINC_LIB_DIR/Applications/freesurfer/mni/lib PERL5LIB /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 GSL_DIR /Applications/freesurfer/lib/gsl TCLLIBPATH /Applications/freesurfer/lib/tcltktixblt/lib MISC_LIB/Applications/freesurfer/lib/misc/lib tcsh: gcc: Command not found. tcsh: gcc: Command not found. FSL_DIR /Applications/freesurfer/fsl Any help at all would be most appreciated. Thanks, Anthony ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit problem
Hi Nick- Yes, I am. If tksurfer would still work on an Intel, then this appears to be the problem. Will wait for a new release. Thanks. Anthony Nick Schmansky wrote: Anthony, Are you using a new Intel-processor based Mac? If so, we don't support that just yet. The 'X Error' message is indicative of this, I think. The 'gcc' message can be ignored, it is an artifact of the FSL startup script (included with the Freesurfer distribution). Nick On Tue, 1 Aug 2006, Anthony Steven Dick wrote: Hello- I have just installed freesurfer. Although tksurfer and tkregister2 seem to work fine, I get the following error message when attempting tkmedit: X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 15 Current serial number in output stream: 15 and I'm not sure if this helps, but when I source the SetUpFreeSurfer.csh script, I get the following: freesurfer-Darwin-tiger-stable-pub-v3.0.3 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast SUBJECTS_DIR/Applications/freesurfer/subjects FUNCTIONALS_DIR /Applications/freesurfer/sessions MINC_BIN_DIR/Applications/freesurfer/mni/bin MINC_LIB_DIR/Applications/freesurfer/mni/lib PERL5LIB /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 GSL_DIR /Applications/freesurfer/lib/gsl TCLLIBPATH /Applications/freesurfer/lib/tcltktixblt/lib MISC_LIB/Applications/freesurfer/lib/misc/lib tcsh: gcc: Command not found. tcsh: gcc: Command not found. FSL_DIR /Applications/freesurfer/fsl Any help at all would be most appreciated. Thanks, Anthony ___ 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] tkmedit problem
Anthony, Are you using a new Intel-processor based Mac? If so, we don't support that just yet. The 'X Error' message is indicative of this, I think. The 'gcc' message can be ignored, it is an artifact of the FSL startup script (included with the Freesurfer distribution). Nick On Tue, 1 Aug 2006, Anthony Steven Dick wrote: Hello- I have just installed freesurfer. Although tksurfer and tkregister2 seem to work fine, I get the following error message when attempting tkmedit: X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 15 Current serial number in output stream: 15 and I'm not sure if this helps, but when I source the SetUpFreeSurfer.csh script, I get the following: freesurfer-Darwin-tiger-stable-pub-v3.0.3 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast SUBJECTS_DIR/Applications/freesurfer/subjects FUNCTIONALS_DIR /Applications/freesurfer/sessions MINC_BIN_DIR/Applications/freesurfer/mni/bin MINC_LIB_DIR/Applications/freesurfer/mni/lib PERL5LIB/Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 GSL_DIR /Applications/freesurfer/lib/gsl TCLLIBPATH /Applications/freesurfer/lib/tcltktixblt/lib MISC_LIB/Applications/freesurfer/lib/misc/lib tcsh: gcc: Command not found. tcsh: gcc: Command not found. FSL_DIR /Applications/freesurfer/fsl Any help at all would be most appreciated. Thanks, Anthony ___ 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] Vanishing Control Points
what volume are you selecting them on? Make sure that it has been "conformed" - that is, that it's 256^3 and 1mm isotropic. On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote: I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why? -Eric ___ 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] Vanishing Control Points (Updated: MNC to MGZ problems)
can you give us details about how you did the conversion? On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote: Upon further investigation it seems to be something wrong with my conversion from MNC to MGZ. I have tried the exact same scan going through Analyze to MGZ and the control points work fine. Has anyone had any issues converting between mnc and mgz? -Eric -Original Message- From: Faden, Eric (NIH/NIMH) [F] Sent: Tue 8/1/2006 9:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Vanishing Control Points I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why? -Eric ___ 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
RE: [Freesurfer] Vanishing Control Points
So my images are 256x256x192 x 1.0mm. One of them works and the other doesn't. Should I add blank slices to bring it to 256? -Eric -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 8/1/2006 2:04 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Vanishing Control Points what volume are you selecting them on? Make sure that it has been "conformed" - that is, that it's 256^3 and 1mm isotropic. On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote: > I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and > try to draw control points I can see a little green cross about 1 voxel down > and to the right of the red cross, but as soon as I move the red cross they > vanish and I can no longer see them. FreeSurfer is saving the points to > tmp/control.dat though they just do not seem to display. Any ideas why? > > -Eric > > ___ > 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] Vanishing Control Points
mri_convert -c worked. -Eric -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 8/1/2006 2:39 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Vanishing Control Points no, you should use mri_convert -c to "conform" them. tkmedit is only guaranteed to work with volumes that have been put through this process. Bruce On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote: > So my images are 256x256x192 x 1.0mm. One of them works and the other > doesn't. Should I add blank slices to bring it to 256? > > -Eric > > -Original Message- > From: Bruce Fischl [mailto:[EMAIL PROTECTED] > Sent: Tue 8/1/2006 2:04 PM > To: Faden, Eric (NIH/NIMH) [F] > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Vanishing Control Points > > what volume are you selecting them on? Make sure that it has been > "conformed" - that is, that it's 256^3 and 1mm isotropic. > On Tue, 1 Aug > 2006, Faden, Eric (NIH/NIMH) [F] wrote: > >> I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain >> and try to draw control points I can see a little green cross about 1 voxel >> down and to the right of the red cross, but as soon as I move the red cross >> they vanish and I can no longer see them. FreeSurfer is saving the points >> to tmp/control.dat though they just do not seem to display. Any ideas why? >> >> -Eric >> >> ___ >> 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] Vanishing Control Points (Updated: MNC to MGZ problems)
So my images come off the scanner as DICOM. Steps For Both: 1) Convert DICOM to ANALYZE 2) Align and Average the scans Steps For Broken: 3) Convert to minc to create a brain mask and do some normalization 4) Use mincedit to fake 1.0mm voxels (mine are actually 0.5 since I am doing monkeys) 5) Use mri_convert to convert MNC to MGZ Steps for Working: 3) Convert Analyze to AFNI 4) Use 3drefit (AFNI) to fake 1.0mm voxels 5) Use mri_convert to convert BRIK to MGZ -Eric -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 8/1/2006 2:27 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Vanishing Control Points (Updated: MNC to MGZ problems) can you give us details about how you did the conversion? On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote: > Upon further investigation it seems to be something wrong with my conversion > from MNC to MGZ. I have tried the exact same scan going through Analyze to > MGZ and the control points work fine. Has anyone had any issues converting > between mnc and mgz? > > -Eric > > -Original Message- > From: Faden, Eric (NIH/NIMH) [F] > Sent: Tue 8/1/2006 9:49 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: [Freesurfer] Vanishing Control Points > > I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and > try to draw control points I can see a little green cross about 1 voxel down > and to the right of the red cross, but as soon as I move the red cross they > vanish and I can no longer see them. FreeSurfer is saving the points to > tmp/control.dat though they just do not seem to display. Any ideas why? > > -Eric > > ___ > 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
RE: [Freesurfer] Vanishing Control Points
no, you should use mri_convert -c to "conform" them. tkmedit is only guaranteed to work with volumes that have been put through this process. Bruce On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote: So my images are 256x256x192 x 1.0mm. One of them works and the other doesn't. Should I add blank slices to bring it to 256? -Eric -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 8/1/2006 2:04 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Vanishing Control Points what volume are you selecting them on? Make sure that it has been "conformed" - that is, that it's 256^3 and 1mm isotropic. On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote: I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why? -Eric ___ 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] Vanishing Control Points (Updated: MNC to MGZ problems)
If you're doing a recon, then there should be an mri/orig.mgz which is conformed (ie, the dimension and voxel size will be 256^3 and 1mm^3) regardless of what you start with. This is what you should be doing all of your operations on (not necessarily orig.mgz, but a conformed volume). doug Faden, Eric (NIH/NIMH) [F] wrote: So my images come off the scanner as DICOM. Steps For Both: 1) Convert DICOM to ANALYZE 2) Align and Average the scans Steps For Broken: 3) Convert to minc to create a brain mask and do some normalization 4) Use mincedit to fake 1.0mm voxels (mine are actually 0.5 since I am doing monkeys) 5) Use mri_convert to convert MNC to MGZ Steps for Working: 3) Convert Analyze to AFNI 4) Use 3drefit (AFNI) to fake 1.0mm voxels 5) Use mri_convert to convert BRIK to MGZ -Eric -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED]] Sent: Tue 8/1/2006 2:27 PM To: Faden, Eric (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Vanishing Control Points (Updated: MNC to MGZ problems) can you give us details about how you did the conversion? On Tue, 1 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote: Upon further investigation it seems to be something wrong with my conversion from MNC to MGZ. I have tried the exact same scan going through Analyze to MGZ and the control points work fine. Has anyone had any issues converting between mnc and mgz? -Eric -Original Message- From: Faden, Eric (NIH/NIMH) [F] Sent: Tue 8/1/2006 9:49 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Vanishing Control Points I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and try to draw control points I can see a little green cross about 1 voxel down and to the right of the red cross, but as soon as I move the red cross they vanish and I can no longer see them. FreeSurfer is saving the points to tmp/control.dat though they just do not seem to display. Any ideas why? -Eric ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Would adjusting watershed parameters change pial surface?
I was wondering if setting the watershed parameters higher and rerunning autorecon2 would expand the pial surface line if the outer rim of the brain is being left out? Or would this not fix the problem? Thanks -- -Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
