Hi,
I have a brand new Macbook pro with the dual-core intel chip. I downloaded and installed the most recent verision of freesurfer. When I run the configuration script I get
source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- 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
Which looks ok, except for not finding gcc. tksurfer seems to run fine, but tkmedit just gives an error:
Kent% tkmedit bert orig.mgz 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
Can anyone help me with this? Thanks . . .
Kent Ogden PhD Associate Professor, Radiology SUNY Upstate Medical University 750 E. Adams Street Syracuse, NY 13210
email: ogdenk@upstate.edu voice: (315) 464-5083 fax: (315) 464-5095
Kent,
Freesurfer does not yet support the new Intel Mac, and the problem with tkmedit is one of the known problems seen with using the powerpc build on such machines. We plan on providing an Intel Mac freesurfer build in the coming months.
The gcc warnings can be ignored.
Nick
On Mon, 2006-08-07 at 21:53 -0400, Kent Ogden wrote:
Hi,
I have a brand new Macbook pro with the dual-core intel chip. I downloaded and installed the most recent verision of freesurfer. When I run the configuration script I get
source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- 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
Which looks ok, except for not finding gcc. tksurfer seems to run fine, but tkmedit just gives an error:
Kent% tkmedit bert orig.mgz 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
Can anyone help me with this? Thanks . . .
Kent Ogden PhD Associate Professor, Radiology SUNY Upstate Medical University 750 E. Adams Street Syracuse, NY 13210
email: ogdenk@upstate.edu voice: (315) 464-5083 fax: (315) 464-5095 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I am working on running some scans through FreeSurfer. I have scans at both 0.5mm and 0.8mm that have all been skull stripped and N3 corrected. The images have good contrast in general and specifically are fairly good in the subcortical regions. I am skipping a bunch of the FreeSurfer pipeline and bringing my scans directly into the mri_normalize step. I have been running it with the -monkey option and a set of about 25 to 50 control points in various areas of white matter. The normalization yields very good contrast in cortex, but basically removes any sign of gray matter in the sub cortical region (e.g. it basically all winds up with a value of 110). Is there any way to combat this problem?
-Eric
Hi Eric,
that's what it's supposed to do. It's really not a bias correction in the way N3 is - it's more of a filtering for the purpose of cortical segmentation.
cheers, Bruce
On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
I am working on running some scans through FreeSurfer. I have scans at both 0.5mm and 0.8mm that have all been skull stripped and N3 corrected. The images have good contrast in general and specifically are fairly good in the subcortical regions. I am skipping a bunch of the FreeSurfer pipeline and bringing my scans directly into the mri_normalize step. I have been running it with the -monkey option and a set of about 25 to 50 control points in various areas of white matter. The normalization yields very good contrast in cortex, but basically removes any sign of gray matter in the sub cortical region (e.g. it basically all winds up with a value of 110). Is there any way to combat this problem?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Right, but is there a way I can fix the subcortical structures so that I can get accurate measures of them?
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 8/9/2006 12:29 PM To: Faden, Eric (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Non Human Primate (Macaque) Subcortical
Hi Eric,
that's what it's supposed to do. It's really not a bias correction in the way N3 is - it's more of a filtering for the purpose of cortical segmentation.
cheers, Bruce
On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
I am working on running some scans through FreeSurfer. I have scans at both 0.5mm and 0.8mm that have all been skull stripped and N3 corrected. The images have good contrast in general and specifically are fairly good in the subcortical regions. I am skipping a bunch of the FreeSurfer pipeline and bringing my scans directly into the mri_normalize step. I have been running it with the -monkey option and a set of about 25 to 50 control points in various areas of white matter. The normalization yields very good contrast in cortex, but basically removes any sign of gray matter in the sub cortical region (e.g. it basically all winds up with a value of 110). Is there any way to combat this problem?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
How do you want to measure them? For example when we generate (human) subcortical segmentations we do *not* use the output of mri_normalize - it is only for cortical.
On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
Right, but is there a way I can fix the subcortical structures so that I can get accurate measures of them?
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 8/9/2006 12:29 PM To: Faden, Eric (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Non Human Primate (Macaque) Subcortical
Hi Eric,
that's what it's supposed to do. It's really not a bias correction in the way N3 is - it's more of a filtering for the purpose of cortical segmentation.
cheers, Bruce
On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
I am working on running some scans through FreeSurfer. I have scans at both 0.5mm and 0.8mm that have all been skull stripped and N3 corrected. The images have good contrast in general and specifically are fairly good in the subcortical regions. I am skipping a bunch of the FreeSurfer pipeline and bringing my scans directly into the mri_normalize step. I have been running it with the -monkey option and a set of about 25 to 50 control points in various areas of white matter. The normalization yields very good contrast in cortex, but basically removes any sign of gray matter in the sub cortical region (e.g. it basically all winds up with a value of 110). Is there any way to combat this problem?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I was going to create surfaces and then export them to Caret to use the Atlas made for Caret.
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 8/9/2006 12:35 PM To: Faden, Eric (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] Non Human Primate (Macaque) Subcortical
How do you want to measure them? For example when we generate (human) subcortical segmentations we do *not* use the output of mri_normalize - it is only for cortical.
On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
Right, but is there a way I can fix the subcortical structures so that I can get accurate measures of them?
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 8/9/2006 12:29 PM To: Faden, Eric (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Non Human Primate (Macaque) Subcortical
Hi Eric,
that's what it's supposed to do. It's really not a bias correction in the way N3 is - it's more of a filtering for the purpose of cortical segmentation.
cheers, Bruce
On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
I am working on running some scans through FreeSurfer. I have scans at both 0.5mm and 0.8mm that have all been skull stripped and N3 corrected. The images have good contrast in general and specifically are fairly good in the subcortical regions. I am skipping a bunch of the FreeSurfer pipeline and bringing my scans directly into the mri_normalize step. I have been running it with the -monkey option and a set of about 25 to 50 control points in various areas of white matter. The normalization yields very good contrast in cortex, but basically removes any sign of gray matter in the sub cortical region (e.g. it basically all winds up with a value of 110). Is there any way to combat this problem?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm still confused. The surfaces will be valid, so Caret should be happy, no?
On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
I was going to create surfaces and then export them to Caret to use the Atlas made for Caret.
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 8/9/2006 12:35 PM To: Faden, Eric (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] Non Human Primate (Macaque) Subcortical
How do you want to measure them? For example when we generate (human) subcortical segmentations we do *not* use the output of mri_normalize - it is only for cortical.
On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
Right, but is there a way I can fix the subcortical structures so that I can get accurate measures of them?
-Eric
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 8/9/2006 12:29 PM To: Faden, Eric (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Non Human Primate (Macaque) Subcortical
Hi Eric,
that's what it's supposed to do. It's really not a bias correction in the way N3 is - it's more of a filtering for the purpose of cortical segmentation.
cheers, Bruce
On Wed, 9 Aug 2006, Faden, Eric (NIH/NIMH) [F] wrote:
I am working on running some scans through FreeSurfer. I have scans at both 0.5mm and 0.8mm that have all been skull stripped and N3 corrected. The images have good contrast in general and specifically are fairly good in the subcortical regions. I am skipping a bunch of the FreeSurfer pipeline and bringing my scans directly into the mri_normalize step. I have been running it with the -monkey option and a set of about 25 to 50 control points in various areas of white matter. The normalization yields very good contrast in cortex, but basically removes any sign of gray matter in the sub cortical region (e.g. it basically all winds up with a value of 110). Is there any way to combat this problem?
-Eric
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Faden, Eric (NIH/NIMH) [F] -
Kent Ogden -
Nick Schmansky