Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt FreeSurferColorLUT.txt. Are my expectations off?
1) In the aparc+aseg.mgz file, intensity values for the cortical labels range from -32768 to 654, with negative values falling in some regions in the left hemisphere. 2) Identical results are obtained if mri_aparc2aseg is used to generate an output file: mri_aparc2aseg --s mysubject --o ./aparc2aseg.mgz 3) Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt
Example values obtained from aparc+aseg.mgz are listed below: lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt) rh.superiortemporal=32767 (expecting 2030)
Although these numerical values do not match the LUT, they are consistent across subjects.
Many Thanks for any insights... Jenifer
Hi Jenifer,
how are you getting those intensity values?
Bruce
On Wed, 22 Oct 2008, Juranek, Jenifer wrote:
Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt FreeSurferColorLUT.txt. Are my expectations off?
- In the aparc+aseg.mgz file, intensity values for the cortical labels range from -32768 to 654, with negative values falling in some regions in the left hemisphere.
- Identical results are obtained if mri_aparc2aseg is used to generate an output file: mri_aparc2aseg --s mysubject --o ./aparc2aseg.mgz
- Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt
Example values obtained from aparc+aseg.mgz are listed below: lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt) rh.superiortemporal=32767 (expecting 2030)
Although these numerical values do not match the LUT, they are consistent across subjects.
Many Thanks for any insights... Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm able to view the intensity values in FSL. Is there another approach I can take to doublecheck?
Jenifer -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, October 22, 2008 4:15 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurferColorLUT & aparc
Hi Jenifer,
how are you getting those intensity values?
Bruce
On Wed, 22 Oct 2008, Juranek, Jenifer wrote:
Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt
FreeSurferColorLUT.txt. Are my expectations off?
- In the aparc+aseg.mgz file, intensity values for the cortical
labels range from -32768 to 654, with negative values falling in some regions in the left hemisphere.
- Identical results are obtained if mri_aparc2aseg is used to
generate an output file: mri_aparc2aseg --s mysubject --o ./aparc2aseg.mgz
- Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt
Example values obtained from aparc+aseg.mgz are listed below: lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt) rh.superiortemporal=32767 (expecting 2030)
Although these numerical values do not match the LUT, they are
consistent across subjects.
Many Thanks for any insights... Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
if you load it in tkmedit is it displayed properly?
On Wed, 22 Oct 2008, Juranek, Jenifer wrote:
I'm able to view the intensity values in FSL. Is there another approach I can take to doublecheck?
Jenifer -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, October 22, 2008 4:15 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurferColorLUT & aparc
Hi Jenifer,
how are you getting those intensity values?
Bruce
On Wed, 22 Oct 2008, Juranek, Jenifer wrote:
Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt
FreeSurferColorLUT.txt. Are my expectations off?
- In the aparc+aseg.mgz file, intensity values for the cortical
labels range from -32768 to 654, with negative values falling in some regions in the left hemisphere.
- Identical results are obtained if mri_aparc2aseg is used to
generate an output file: mri_aparc2aseg --s mysubject --o ./aparc2aseg.mgz
- Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt
Example values obtained from aparc+aseg.mgz are listed below: lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt) rh.superiortemporal=32767 (expecting 2030)
Although these numerical values do not match the LUT, they are
consistent across subjects.
Many Thanks for any insights... Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, the correct Sgmtn label is displayed in the TkMedit Tools
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, October 22, 2008 4:30 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurferColorLUT & aparc
if you load it in tkmedit is it displayed properly?
On Wed, 22 Oct 2008, Juranek, Jenifer wrote:
I'm able to view the intensity values in FSL. Is there another
approach
I can take to doublecheck?
Jenifer -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, October 22, 2008 4:15 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurferColorLUT & aparc
Hi Jenifer,
how are you getting those intensity values?
Bruce
On Wed, 22 Oct 2008, Juranek, Jenifer wrote:
Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt
FreeSurferColorLUT.txt. Are my expectations off?
- In the aparc+aseg.mgz file, intensity values for the cortical
labels range from -32768 to 654, with negative values falling in some regions in the left hemisphere.
- Identical results are obtained if mri_aparc2aseg is used to
generate an output file: mri_aparc2aseg --s mysubject --o ./aparc2aseg.mgz
- Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt
Example values obtained from aparc+aseg.mgz are listed below: lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt) rh.superiortemporal=32767 (expecting 2030)
Although these numerical values do not match the LUT, they are
consistent across subjects.
Many Thanks for any insights... Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
and how do you get it into FSL? On Wed, 22 Oct 2008, Juranek, Jenifer wrote:
yes, the correct Sgmtn label is displayed in the TkMedit Tools
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, October 22, 2008 4:30 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] FreeSurferColorLUT & aparc
if you load it in tkmedit is it displayed properly?
On Wed, 22 Oct 2008, Juranek, Jenifer wrote:
I'm able to view the intensity values in FSL. Is there another
approach
I can take to doublecheck?
Jenifer -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, October 22, 2008 4:15 PM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FreeSurferColorLUT & aparc
Hi Jenifer,
how are you getting those intensity values?
Bruce
On Wed, 22 Oct 2008, Juranek, Jenifer wrote:
Hi, Running fsv405 on RHEL5. I've encountered some unexpected numerical values wrt
FreeSurferColorLUT.txt. Are my expectations off?
- In the aparc+aseg.mgz file, intensity values for the cortical
labels range from -32768 to 654, with negative values falling in some regions in the left hemisphere.
- Identical results are obtained if mri_aparc2aseg is used to
generate an output file: mri_aparc2aseg --s mysubject --o ./aparc2aseg.mgz
- Values of aseg.mgz map perfectly well to FreeSurferColorLUT.txt
Example values obtained from aparc+aseg.mgz are listed below: lh.superiortemporal=484 (expecting 1030 from FreeSurferColorLUT.txt) rh.superiortemporal=32767 (expecting 2030)
Although these numerical values do not match the LUT, they are
consistent across subjects.
Many Thanks for any insights... Jenifer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Juranek, Jenifer