Hello,
I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3.
When I ran mri_cvs_check, my feedback was I needed to find "mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.htm...
mri_cvs_register kicks off well, but eventually it ends with:
"mris_resample: Command not found."
I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly?
I have attached a log file in case this helps.
Cheers, Daniel
Hi Daniel,
What operating system are you using?
Lilla
On Tue, 28 May 2013, Barron, Daniel S wrote:
Hello,
I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3.
When I ran mri_cvs_check, my feedback was I needed to find "mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.htm...
mri_cvs_register kicks off well, but eventually it ends with:
"mris_resample: Command not found."
I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly?
I have attached a log file in case this helps.
Cheers, Daniel
Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel ________________________________________ From: Lilla Zollei [lzollei@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found.
Hi Daniel,
What operating system are you using?
Lilla
On Tue, 28 May 2013, Barron, Daniel S wrote:
Hello,
I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3.
When I ran mri_cvs_check, my feedback was I needed to find "mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.htm...
mri_cvs_register kicks off well, but eventually it ends with:
"mris_resample: Command not found."
I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly?
I have attached a log file in case this helps.
Cheers, Daniel
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hello Daniel,
This is a confirmed issue with the 64bit Mac build. A patch to fix the issue will be available shortly (~hours). I will email the list and you personally once it is available. Sorry for the inconvenience.
-Zeke
On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel ________________________________________ From: Lilla Zollei [lzollei@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found.
Hi Daniel,
What operating system are you using?
Lilla
On Tue, 28 May 2013, Barron, Daniel S wrote:
Hello,
I am trying to perform an inter-subject registration using mri_cvs_register on version 5.3.
When I ran mri_cvs_check, my feedback was I needed to find "mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.htm...
mri_cvs_register kicks off well, but eventually it ends with:
"mris_resample: Command not found."
I go into my $FREESURFER_HOME/bin directory and note that mris_resample is truly not there. Did I not install 5.3 properly?
I have attached a log file in case this helps.
Cheers, Daniel
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Daniel, Stefano, Others,
A patch is now available for the "mris_resample : Command not found" error you encountered.
Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
Feel free to contact me if you have any additional questions/issues.
-Zeke
-------- Original Message -------- Subject: Re: [Freesurfer] mris_resample: Command not found. Date: Tue, 28 May 2013 11:41:21 -0400 From: Z K zkaufman@nmr.mgh.harvard.edu To: Barron, Daniel S barrond@livemail.uthscsa.edu CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu, Lilla Zollei lzollei@nmr.mgh.harvard.edu
Hello Daniel,
This is a confirmed issue with the 64bit Mac build. A patch to fix the issue will be available shortly (~hours). I will email the list and you personally once it is available. Sorry for the inconvenience.
-Zeke
On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel ________________________________________ From: Lilla Zollei [lzollei@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found. Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote:
Hello, I am trying to perform an inter-subject registration using
mri_cvs_register on version 5.3.
When I ran mri_cvs_check, my feedback was I needed to find
"mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.htm...
mri_cvs_register kicks off well, but eventually it ends with: "mris_resample: Command not found." I go into my $FREESURFER_HOME/bin directory and note that mris_resample
is truly not there. Did I not install 5.3 properly?
I have attached a log file in case this helps. Cheers, Daniel
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
dispose of the 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
Thanks for the path, Zeke.
Because it didn't download as an executable file to my computer, I used "chmod +x ~/mris_resample" (FYI for others?)
It looks to be running normally. Will report back when finished!
Thanks again, Daniel
On May 28, 2013, at 11:25 PM, zkaufman@nmr.mgh.harvard.edu wrote:
Daniel, Stefano, Others,
A patch is now available for the "mris_resample : Command not found" error you encountered.
Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
Feel free to contact me if you have any additional questions/issues.
-Zeke
-------- Original Message -------- Subject: Re: [Freesurfer] mris_resample: Command not found. Date: Tue, 28 May 2013 11:41:21 -0400 From: Z K zkaufman@nmr.mgh.harvard.edu To: Barron, Daniel S barrond@livemail.uthscsa.edu CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu, Lilla Zollei lzollei@nmr.mgh.harvard.edu
Hello Daniel,
This is a confirmed issue with the 64bit Mac build. A patch to fix the issue will be available shortly (~hours). I will email the list and you personally once it is available. Sorry for the inconvenience.
-Zeke
On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel ________________________________________ From: Lilla Zollei [lzollei@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found. Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote:
Hello, I am trying to perform an inter-subject registration using
mri_cvs_register on version 5.3.
When I ran mri_cvs_check, my feedback was I needed to find
"mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.htm...
mri_cvs_register kicks off well, but eventually it ends with: "mris_resample: Command not found." I go into my $FREESURFER_HOME/bin directory and note that mris_resample
is truly not there. Did I not install 5.3 properly?
I have attached a log file in case this helps. Cheers, Daniel
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
dispose of the 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
Hi All,
Was able to register 3 subjects to a common space with really great accuracy (both of the overall volumes and of the aseg files).
Note: cvs_register takes up quite a bit of RAM (how much exactly?) which caused my desktop to slow and, essentially, crash. Ended up running them on the server.
Question: While a description of the output is given on the wiki, I struggled to tease out the details. Can I assume that el_reg_toXX.mgz is the final output file? I was somewhat confused because I assume "el" means elastic? I am looking for the final registration file that incorporates both surfaces and volumes.
Again, thank you very much for the patch and for the excellent software.
Cheers, Daniel
On May 28, 2013, at 11:54 PM, Barron, Daniel S wrote:
Thanks for the path, Zeke.
Because it didn't download as an executable file to my computer, I used "chmod +x ~/mris_resample" (FYI for others?)
It looks to be running normally. Will report back when finished!
Thanks again, Daniel
On May 28, 2013, at 11:25 PM, zkaufman@nmr.mgh.harvard.edu wrote:
Daniel, Stefano, Others,
A patch is now available for the "mris_resample : Command not found" error you encountered.
Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
Feel free to contact me if you have any additional questions/issues.
-Zeke
-------- Original Message -------- Subject: Re: [Freesurfer] mris_resample: Command not found. Date: Tue, 28 May 2013 11:41:21 -0400 From: Z K zkaufman@nmr.mgh.harvard.edu To: Barron, Daniel S barrond@livemail.uthscsa.edu CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu, Lilla Zollei lzollei@nmr.mgh.harvard.edu
Hello Daniel,
This is a confirmed issue with the 64bit Mac build. A patch to fix the issue will be available shortly (~hours). I will email the list and you personally once it is available. Sorry for the inconvenience.
-Zeke
On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel ________________________________________ From: Lilla Zollei [lzollei@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found. Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote:
Hello, I am trying to perform an inter-subject registration using
mri_cvs_register on version 5.3.
When I ran mri_cvs_check, my feedback was I needed to find
"mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.htm...
mri_cvs_register kicks off well, but eventually it ends with: "mris_resample: Command not found." I go into my $FREESURFER_HOME/bin directory and note that mris_resample
is truly not there. Did I not install 5.3 properly?
I have attached a log file in case this helps. Cheers, Daniel
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
dispose of the 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Daniel,
All the information wrt memory and file naming conventions is described in: mri_cvs_register --help
The final output file should be named final*norm.mgz
Lilla
On Mon, 3 Jun 2013, Barron, Daniel S wrote:
Hi All,
Was able to register 3 subjects to a common space with really great accuracy (both of the overall volumes and of the aseg files).
Note: cvs_register takes up quite a bit of RAM (how much exactly?) which caused my desktop to slow and, essentially, crash. Ended up running them on the server.
Question: While a description of the output is given on the wiki, I struggled to tease out the details. Can I assume that el_reg_toXX.mgz is the final output file? I was somewhat confused because I assume "el" means elastic? I am looking for the final registration file that incorporates both surfaces and volumes.
Again, thank you very much for the patch and for the excellent software.
Cheers, Daniel
On May 28, 2013, at 11:54 PM, Barron, Daniel S wrote:
Thanks for the path, Zeke.
Because it didn't download as an executable file to my computer, I used "chmod +x ~/mris_resample" (FYI for others?)
It looks to be running normally. Will report back when finished!
Thanks again, Daniel
On May 28, 2013, at 11:25 PM, zkaufman@nmr.mgh.harvard.edu wrote:
Daniel, Stefano, Others,
A patch is now available for the "mris_resample : Command not found" error you encountered.
Simply download the file from the following link and place it in your $FREESURFER_HOME/bin directory:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample
Feel free to contact me if you have any additional questions/issues.
-Zeke
-------- Original Message -------- Subject: Re: [Freesurfer] mris_resample: Command not found. Date: Tue, 28 May 2013 11:41:21 -0400 From: Z K zkaufman@nmr.mgh.harvard.edu To: Barron, Daniel S barrond@livemail.uthscsa.edu CC: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu, Lilla Zollei lzollei@nmr.mgh.harvard.edu
Hello Daniel,
This is a confirmed issue with the 64bit Mac build. A patch to fix the issue will be available shortly (~hours). I will email the list and you personally once it is available. Sorry for the inconvenience.
-Zeke
On 05/28/2013 11:36 AM, Barron, Daniel S wrote:
Hi Lilla, I'm using OSX 10.8.3 Thanks, Daniel ________________________________________ From: Lilla Zollei [lzollei@nmr.mgh.harvard.edu] Sent: Tuesday, May 28, 2013 10:04 AM To: Barron, Daniel S Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: mris_resample: Command not found. Hi Daniel, What operating system are you using? Lilla On Tue, 28 May 2013, Barron, Daniel S wrote:
Hello, I am trying to perform an inter-subject registration using
mri_cvs_register on version 5.3.
When I ran mri_cvs_check, my feedback was I needed to find
"mri_cvs_register.settings.txt" but I didn't worry about this per Lilla's post: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-April/023445.htm...
mri_cvs_register kicks off well, but eventually it ends with: "mris_resample: Command not found." I go into my $FREESURFER_HOME/bin directory and note that mris_resample
is truly not there. Did I not install 5.3 properly?
I have attached a log file in case this helps. Cheers, Daniel
The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
dispose of the 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Barron, Daniel S -
Lilla Zollei -
Z K -
zkaufman＠nmr.mgh.harvard.edu