FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-leopard-stable-pub-v4.0.3
Kernel info: Darwin 9.0.0 i386 ___
I recently updated to the newest release of freesurfer because for some reason I was unable to run qdec with 4.0.2. Though it appears that everything is setup exactly as it was before, I cannot execute any of the GUI (tkmedit, tksurfer, or qdec)
I tried using the tutorial dataset to debug this. Below is an example command:
tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
Regardless of what I try to run, I get the following error:
Couldn't create output file .xdebug_tkmeditX Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 17 Current serial number in output stream: 17
I already looked in the archives. I do have the most up to date version of X11. I am running this on my local machine, not via ssh, so this is not a display problem. All of my necessary variables are set (SUBJECTS_DIR, FREESURFER_HOME) and I have sourced $FREESURFER_HOME/ SetUpFreeSurfer.csh.
Thnaks you in advance for your help.
Jennifer Bramen
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Jennifer,
I think you have the PowerPC build, but your machine has an Intel processor. Try getting the one named:
freesurfer-Darwin-leopard-i686-stable-pub-v4.0.3-full.dmg
Although in principle (as stated by Apple) PowerPC code can be emulated on the Intel processor, in practice it looks like it doesnt work in all instances.
Nick
On Fri, 2008-04-25 at 14:05 -0700, Jennifer Bramen wrote:
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-leopard-stable-pub-v4.0.3
Kernel info: Darwin 9.0.0 i386 ___
I recently updated to the newest release of freesurfer because for some reason I was unable to run qdec with 4.0.2. Though it appears that everything is setup exactly as it was before, I cannot execute any of the GUI (tkmedit, tksurfer, or qdec)
I tried using the tutorial dataset to debug this. Below is an example command:
tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt
Regardless of what I try to run, I get the following error:
Couldn't create output file .xdebug_tkmeditX Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 128 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 17 Current serial number in output stream: 17
I already looked in the archives. I do have the most up to date version of X11. I am running this on my local machine, not via ssh, so this is not a display problem. All of my necessary variables are set (SUBJECTS_DIR, FREESURFER_HOME) and I have sourced $FREESURFER_HOME/ SetUpFreeSurfer.csh.
Thnaks you in advance for your help.
Jennifer Bramen
IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Freesurfer Users,
This may be a newbie question. I am trying to evaluate regional volumes. I have been able to tabulate the gray matter volumes, but cannot figure out how to tabulate all the white matter volumes. I see that in individual folders, there is a file called wmparc.stats. Do any of the tools query this file, or will I need to pull the data manually? Inside this file, I see some of the regions listed as wm-?h- <regionname>. Next to these are sometimes a lot of zeros and sometimes a bunch of values. I am wondering why so many of these do not have values associated with them. I am also wondering why only some of the regions listed in this file are labeled wm, when the file suggests it contains white matter stats...
If there is somewhere on the site that explains white matter volumetric analyses, could someone please send me the link?
Thank you
Jennifer Bramen
---------------------------------------------------------- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. ----------------------------------------------------------
I posted the below question regarding white matter volumes to the list last Friday. I think it fell through the cracks because I sent it out in the late afternoon, and was hoping someone could help me understand 1) the outputs of indicvidual wmparc.stats files and 2) how to tabulate these data like we can with gray matter volumes. Thanks again.
Jen
Hi Freesurfer Users,
This may be a newbie question. I am trying to evaluate regional volumes. I have been able to tabulate the gray matter volumes, but cannot figure out how to tabulate all the white matter volumes. I see that in individual folders, there is a file called wmparc.stats. Do any of the tools query this file, or will I need to pull the data manually? Inside this file, I see some of the regions listed as wm-? h-<regionname>. Next to these are sometimes a lot of zeros and sometimes a bunch of values. I am wondering why so many of these do not have values associated with them. I am also wondering why only some of the regions listed in this file are labeled wm, when the file suggests it contains white matter stats...
If there is somewhere on the site that explains white matter volumetric analyses, could someone please send me the link?
Thank you
Jennifer Bramen
IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---------------------------------------------------------- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. ----------------------------------------------------------
Hi Jen,
Doug is out of town at the fBIRN meeting, and he's the one that will answer this so you might have to wait a bit.
cheers, Bruce On Tue, 29 Apr 2008, Jennifer Bramen wrote:
I posted the below question regarding white matter volumes to the list last Friday. I think it fell through the cracks because I sent it out in the late afternoon, and was hoping someone could help me understand 1) the outputs of indicvidual wmparc.stats files and 2) how to tabulate these data like we can with gray matter volumes. Thanks again.
Jen
Hi Freesurfer Users,
This may be a newbie question. I am trying to evaluate regional volumes. I have been able to tabulate the gray matter volumes, but cannot figure out how to tabulate all the white matter volumes. I see that in individual folders, there is a file called wmparc.stats. Do any of the tools query this file, or will I need to pull the data manually? Inside this file, I see some of the regions listed as wm-?h-<regionname>. Next to these are sometimes a lot of zeros and sometimes a bunch of values. I am wondering why so many of these do not have values associated with them. I am also wondering why only some of the regions listed in this file are labeled wm, when the file suggests it contains white matter stats...
If there is somewhere on the site that explains white matter volumetric analyses, could someone please send me the link?
Thank you
Jennifer Bramen
IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Jennifer Bramen -
Nick Schmansky