Hello,
I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html
When I run xhemireg I receive the error "ERROR: Option --keep-precision unknown"
I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions?
Andrew
I just put a new version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
doug
On 10/1/12 10:56 PM, Andrew Bock wrote:
Hello,
I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html
When I run xhemireg I receive the error "ERROR: Option --keep-precision unknown"
I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions?
Andrew
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug!
However, now I'm getting the following error:
*Resampling Output registration matrix is identity
mri_vol2vol done ERROR: canot find norm*
I am running:
*xhemireg --s fsaverage --reg*
Any suggestions? Should I run the following from $SUBJECTS_DIR/fsaverage/mri/?
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 --uchar transforms/talairach.xfm mri_ca_normalize -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz
Andrew
On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
I just put a new version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
doug
On 10/1/12 10:56 PM, Andrew Bock wrote:
Hello,
I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html
When I run xhemireg I receive the error "ERROR: Option --keep-precision unknown"
I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions?
Andrew
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
when did you update the xhemi scripts last? Do a search on our wiki for xhemi to get pointers to the most recent ones
On 10/02/2012 01:59 PM, Andrew Bock wrote:
Thanks Doug!
However, now I'm getting the following error:
/Resampling Output registration matrix is identity
mri_vol2vol done ERROR: canot find norm/
I am running:
/xhemireg --s fsaverage --reg/
Any suggestions? Should I run the following from $SUBJECTS_DIR/fsaverage/mri/?
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 --uchar transforms/talairach.xfm mri_ca_normalize -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz
Andrew
On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I just put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol doug On 10/1/12 10:56 PM, Andrew Bock wrote:Hello, I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html When I run xhemireg I receive the error "ERROR: Option --keep-precision unknown" I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions? Andrew _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
I updated all the xhemi scripts following: http://www.freesurfer.net/fswiki/Xhemi but unfortunately the problem persists for fsaverage, since norm.mgz does not exist for fsaverage. I'm going to try creating norm.mgz for fsaverage to see if xhemireg works. Even if it doesn't, xhemireg does work for my other subjects, so I'll be able to find a solution.
Thanks for your help,
Andrew
On Tue, Oct 2, 2012 at 12:19 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
when did you update the xhemi scripts last? Do a search on our wiki for xhemi to get pointers to the most recent ones
On 10/02/2012 01:59 PM, Andrew Bock wrote:
Thanks Doug!
However, now I'm getting the following error:
/Resampling
Output registration matrix is identity
mri_vol2vol done ERROR: canot find norm/
I am running:
/xhemireg --s fsaverage --reg/
Any suggestions? Should I run the following from $SUBJECTS_DIR/fsaverage/mri/?
mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 --uchar transforms/talairach.xfm mri_ca_normalize -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_* *all_2008-03-26.gca transforms/talairach.lta norm.mgz
Andrew
On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
I just put a new version here: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/mri_vol2volftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
doug On 10/1/12 10:56 PM, Andrew Bock wrote:Hello, I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2012-**June/024182.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html
When I run xhemireg I receive the error "ERROR: Option --keep-precision unknown" I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions? Andrew ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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<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.-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
why are you running xhemireg for fsaverage?
On 10/02/2012 06:04 PM, Andrew Bock wrote:
I updated all the xhemi scripts following: http://www.freesurfer.net/fswiki/Xhemi but unfortunately the problem persists for fsaverage, since norm.mgz does not exist for fsaverage. I'm going to try creating norm.mgz for fsaverage to see if xhemireg works. Even if it doesn't, xhemireg does work for my other subjects, so I'll be able to find a solution.
Thanks for your help,
Andrew
On Tue, Oct 2, 2012 at 12:19 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
when did you update the xhemi scripts last? Do a search on our wiki for xhemi to get pointers to the most recent ones On 10/02/2012 01:59 PM, Andrew Bock wrote: Thanks Doug! However, now I'm getting the following error: /Resampling Output registration matrix is identity mri_vol2vol done ERROR: canot find norm/ I am running: /xhemireg --s fsaverage --reg/ Any suggestions? Should I run the following from $SUBJECTS_DIR/fsaverage/mri/? mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 --uchar transforms/talairach.xfm mri_ca_normalize -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz Andrew On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: I just put a new version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol doug On 10/1/12 10:56 PM, Andrew Bock wrote: Hello, I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html When I run xhemireg I receive the error "ERROR: Option --keep-precision unknown" I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions? Andrew _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
I have a custom overlay on the left hemisphere of fsaverage, I wanted to resample that overlay onto the right hemisphere. I thought it would save time to run xhemireg once for fsaverage, and then resample the left and right fsaverage overlays onto the left and right hemispheres for all my subjects.
Instead, I can run xhemireg on all my subjects, and then resample the left hemisphere overlay of fsaverage to the left and /xhemi (right) hemispheres for each subject. It will take a bit longer, but it should be fine.
Andrew
On Tue, Oct 2, 2012 at 3:05 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
why are you running xhemireg for fsaverage?
On 10/02/2012 06:04 PM, Andrew Bock wrote:
I updated all the xhemi scripts following: http://www.freesurfer.net/** fswiki/Xhemi http://www.freesurfer.net/fswiki/Xhemi but unfortunately the problem persists for fsaverage, since norm.mgz does not exist for fsaverage. I'm going to try creating norm.mgz for fsaverage to see if xhemireg works. Even if it doesn't, xhemireg does work for my other subjects, so I'll be able to find a solution.
Thanks for your help,
Andrew
On Tue, Oct 2, 2012 at 12:19 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
when did you update the xhemi scripts last? Do a search on our wiki for xhemi to get pointers to the most recent ones On 10/02/2012 01:59 PM, Andrew Bock wrote: Thanks Doug! However, now I'm getting the following error: /Resampling Output registration matrix is identity mri_vol2vol done ERROR: canot find norm/ I am running: /xhemireg --s fsaverage --reg/ Any suggestions? Should I run the following from $SUBJECTS_DIR/fsaverage/mri/? mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 --uchar transforms/talairach.xfm mri_ca_normalize -mask brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_**all_2008-03-26.gca transforms/talairach.lta norm.mgz Andrew On Mon, Oct 1, 2012 at 8:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote:
I just put a new version here: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/mri_vol2volftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
doug On 10/1/12 10:56 PM, Andrew Bock wrote: Hello, I'm having a problem similar to the one outlined here: https://mail.nmr.mgh.harvard.**edu/pipermail/freesurfer/2012-**June/024182.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024182.html
When I run xhemireg I receive the error "ERROR: Option --keep-precision unknown" I looked for the newer version of mri_vol2vol described in the previous post, but could not find it on the ftp site. Any suggestions? Andrew ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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<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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Andrew Bock -
Douglas Greve -
Douglas N Greve