Hi,
I am attempting to move an annotation file from the right to left hemisphere. I have run xhemi registration with:
surfreg —s $subj —t fsaverage_sym —lhrh surfreg —s $subj —t fsaverage_sym —lhrh —xhemi
The annotation file is rh.myclusters.annot in the $subj/xhemi/label subdirectory. I've tried using both mri_surf2surf and mris_apply_reg:
mri_surf2surf --srcsubject s1315_base/xhemi --sval-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --tval $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --trgsubject s1315_base --srchemi rh --trghemi lh --srcsurfreg fsaverage_sym.sphere.reg --trgsurfreg fsaverage_sym.sphere.reg
mris_apply_reg --src-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --trg $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --streg $SUBJECTS_DIR/s1315_base/xhemi/surf/rh.fsaverage_sym.sphere.reg $SUBJECTS_DIR/s1315_base/surf/lh.fsaverage_sym.sphere.reg --no-rev
I've tried mris_apply_reg with and without the '--no-rev' flag. The output from each of these commands is the same: the clusters are on the medial aspect of the LH. They were clusters in the supramarginal and temporal regions on the RH, so I was expecting them to be in the same regions on the LH.
Thanks, Peggy
Use mris_apply_reg. You can get a copy here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg
Run with --help to get docs doug
On 12/17/2015 01:02 PM, Peggy Skelly wrote:
Hi,
I am attempting to move an annotation file from the right to left hemisphere. I have run xhemi registration with:
surfreg —s $subj —t fsaverage_sym —lhrh surfreg —s $subj —t fsaverage_sym —lhrh —xhemi
The annotation file is rh.myclusters.annot in the $subj/xhemi/label subdirectory. I've tried using both mri_surf2surf and mris_apply_reg:
mri_surf2surf --srcsubject s1315_base/xhemi --sval-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --tval $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --trgsubject s1315_base --srchemi rh --trghemi lh --srcsurfreg fsaverage_sym.sphere.reg --trgsurfreg fsaverage_sym.sphere.reg
mris_apply_reg --src-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --trg $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --streg $SUBJECTS_DIR/s1315_base/xhemi/surf/rh.fsaverage_sym.sphere.reg $SUBJECTS_DIR/s1315_base/surf/lh.fsaverage_sym.sphere.reg --no-rev
I've tried mris_apply_reg with and without the '--no-rev' flag. The output from each of these commands is the same: the clusters are on the medial aspect of the LH. They were clusters in the supramarginal and temporal regions on the RH, so I was expecting them to be in the same regions on the LH.
Thanks, Peggy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I downloaded the file, but cannot get it to run. I changed permissions to make it executable, but I get
-bash: ./mris_apply_reg: cannot execute binary file
I'm using Mac OS X 10.11
Peggy
On Thu, Dec 17, 2015 at 4:24 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Use mris_apply_reg. You can get a copy here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg
Run with --help to get docs doug
On 12/17/2015 01:02 PM, Peggy Skelly wrote:
Hi,
I am attempting to move an annotation file from the right to left hemisphere. I have run xhemi registration with:
surfreg —s $subj —t fsaverage_sym —lhrh surfreg —s $subj —t fsaverage_sym —lhrh —xhemi
The annotation file is rh.myclusters.annot in the $subj/xhemi/label subdirectory. I've tried using both mri_surf2surf and mris_apply_reg:
mri_surf2surf --srcsubject s1315_base/xhemi --sval-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --tval $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --trgsubject s1315_base --srchemi rh --trghemi lh --srcsurfreg fsaverage_sym.sphere.reg --trgsurfreg fsaverage_sym.sphere.reg
mris_apply_reg --src-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --trg $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --streg $SUBJECTS_DIR/s1315_base/xhemi/surf/rh.fsaverage_sym.sphere.reg $SUBJECTS_DIR/s1315_base/surf/lh.fsaverage_sym.sphere.reg --no-rev
I've tried mris_apply_reg with and without the '--no-rev' flag. The output from each of these commands is the same: the clusters are on the medial aspect of the LH. They were clusters in the supramarginal and temporal regions on the RH, so I was expecting them to be in the same regions on the LH.
Thanks, Peggy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg.mac
On 12/18/15 10:53 AM, Peggy Skelly wrote:
I downloaded the file, but cannot get it to run. I changed permissions to make it executable, but I get
-bash: ./mris_apply_reg: cannot execute binary file
I'm using Mac OS X 10.11
Peggy
On Thu, Dec 17, 2015 at 4:24 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Use mris_apply_reg. You can get a copy here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg Run with --help to get docs doug On 12/17/2015 01:02 PM, Peggy Skelly wrote: > Hi, > > I am attempting to move an annotation file from the right to left > hemisphere. I have run xhemi registration with: > > surfreg —s $subj —t fsaverage_sym —lhrh > surfreg —s $subj —t fsaverage_sym —lhrh —xhemi > > The annotation file is rh.myclusters.annot in the $subj/xhemi/label > subdirectory. I've tried using both mri_surf2surf and mris_apply_reg: > > mri_surf2surf --srcsubject s1315_base/xhemi --sval-annot > $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --tval > $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --trgsubject > s1315_base --srchemi rh --trghemi lh --srcsurfreg > fsaverage_sym.sphere.reg --trgsurfreg fsaverage_sym.sphere.reg > > mris_apply_reg --src-annot > $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --trg > $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --streg > $SUBJECTS_DIR/s1315_base/xhemi/surf/rh.fsaverage_sym.sphere.reg > $SUBJECTS_DIR/s1315_base/surf/lh.fsaverage_sym.sphere.reg --no-rev > > I've tried mris_apply_reg with and without the '--no-rev' flag. The > output from each of these commands is the same: the clusters are on > the medial aspect of the LH. They were clusters in the supramarginal > and temporal regions on the RH, so I was expecting them to be in the > same regions on the LH. > > Thanks, > Peggy > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That version works!
I actually already was using that version since I downloaded a recent dev version of freesurfer. My difficulty ended up being specifying the correct source-target registrations. For future reference, the following command moves rh annotations in subject's xhemi directory to the left hemisphere:
mris_apply_reg --src-annot $subj/xhemi/label/.rh.myclusters.annot --trg $subj/label/lh.mymovedclusters.annot \ --streg $subj/surf/lh.fsaverage_sym.sphere.reg $subj/surf/lh.fsaverage_sym.sphere.reg
with the registration previously computed with surfreg --s $subj --t fsaverage_sym --lhrh
Peggy
On Fri, Dec 18, 2015 at 11:17 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Try this one
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg.mac
On 12/18/15 10:53 AM, Peggy Skelly wrote:
I downloaded the file, but cannot get it to run. I changed permissions to make it executable, but I get
-bash: ./mris_apply_reg: cannot execute binary file
I'm using Mac OS X 10.11
Peggy
On Thu, Dec 17, 2015 at 4:24 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Use mris_apply_reg. You can get a copy here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg
Run with --help to get docs doug
On 12/17/2015 01:02 PM, Peggy Skelly wrote:
Hi,
I am attempting to move an annotation file from the right to left hemisphere. I have run xhemi registration with:
surfreg —s $subj —t fsaverage_sym —lhrh surfreg —s $subj —t fsaverage_sym —lhrh —xhemi
The annotation file is rh.myclusters.annot in the $subj/xhemi/label subdirectory. I've tried using both mri_surf2surf and mris_apply_reg:
mri_surf2surf --srcsubject s1315_base/xhemi --sval-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --tval $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --trgsubject s1315_base --srchemi rh --trghemi lh --srcsurfreg fsaverage_sym.sphere.reg --trgsurfreg fsaverage_sym.sphere.reg
mris_apply_reg --src-annot $SUBJECTS_DIR/s1315_base/xhemi/label/rh.myclusters.annot --trg $SUBJECTS_DIR/s1315_base/label/lh.myclusters.annot --streg $SUBJECTS_DIR/s1315_base/xhemi/surf/rh.fsaverage_sym.sphere.reg $SUBJECTS_DIR/s1315_base/surf/lh.fsaverage_sym.sphere.reg --no-rev
I've tried mris_apply_reg with and without the '--no-rev' flag. The output from each of these commands is the same: the clusters are on the medial aspect of the LH. They were clusters in the supramarginal and temporal regions on the RH, so I was expecting them to be in the same regions on the LH.
Thanks, Peggy
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
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.
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Peggy Skelly