Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help.
I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be.
I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain.
I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register.
I've done:
cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right
I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum: 1) mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere lh.sphere.left_right 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right rh.sphere.left_right --trg rh.lh.source.label
No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped ROIs.
Thanks for your help!
Joe
I think mri_label2label with the sphere from the left right registration should work Bruce
On Oct 11, 2017, at 5:43 PM, Neuro Lists neuro.mailing.lists@gmail.com wrote:
Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help.
I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be.
I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain.
I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register.
I've done:
cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right
I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum:
- mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere lh.sphere.left_right
- mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right
rh.sphere.left_right --trg rh.lh.source.label
No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped ROIs.
Thanks for your help!
Joe _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try
mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere.left_right rh.sphere
On 10/11/17 5:43 PM, Neuro Lists wrote:
Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help.
I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be.
I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain.
I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register.
I've done:
cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right
I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum:
- mris_apply_reg --src-label your.lh.label --trg your.rh.label
-streg lh.sphere lh.sphere.left_right 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right rh.sphere.left_right --trg rh.lh.source.label
No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped ROIs.
Thanks for your help!
Joe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug and Bruce, I forgot to mention that I had tried that as well but without success. As a sanity check, tried flipping a label from the 'bert' subject and it still comes out wrong. I've uploaded a screen shot of the result:
Thank you for any input you might have!
These were the exact steps the following (I also tried playing around with the options to --streg but without luck):
cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right cd ../label
mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere
$Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $
cwd /home/joe/subjects/bert/label
cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere
sysname Linux
hostname computer
machine x86_64
user joe
srcvalfile (null)
trgvalfile lh_flip.BA45.label
nsurfs 2
jac 0
revmap 0
1 Loading ../surf/lh.sphere.left_right
2 Loading ../surf/rh.sphere
Loading label lh.BA45.label
4060 points in input label
MRISapplyReg: nsurfs = 2, revmap=0, jac=0, hash=1
MRISapplyReg: building hash tables (res=16).
MRISapplyReg: Forward Loop (133299)
MRISapplyReg: Dividing by number of hits (133299)
MRISapplyReg: nSrcLost = 38462
4505 points in output label
mris_apply_reg done
On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Try
mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere.left_right rh.sphere
On 10/11/17 5:43 PM, Neuro Lists wrote:
Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help.
I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be.
I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain.
I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register.
I've done:
cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right
I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum:
- mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg
lh.sphere lh.sphere.left_right 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right rh.sphere.left_right --trg rh.lh.source.label
No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped ROIs.
Thanks for your help!
Joe
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.
Hi all, I was just wondering if there was any further insight into what I might be doing wrong on this.
Thanks again!
On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists <neuro.mailing.lists@gmail.com
wrote:
Hi Doug and Bruce, I forgot to mention that I had tried that as well but without success. As a sanity check, tried flipping a label from the 'bert' subject and it still comes out wrong. I've uploaded a screen shot of the result:
Thank you for any input you might have!
These were the exact steps the following (I also tried playing around with the options to --streg but without luck):
cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right cd ../label
mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere
$Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $
cwd /home/joe/subjects/bert/label
cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere
sysname Linux
hostname computer
machine x86_64
user joe
srcvalfile (null)
trgvalfile lh_flip.BA45.label
nsurfs 2
jac 0
revmap 0
1 Loading ../surf/lh.sphere.left_right
2 Loading ../surf/rh.sphere
Loading label lh.BA45.label
4060 points in input label
MRISapplyReg: nsurfs = 2, revmap=0, jac=0, hash=1
MRISapplyReg: building hash tables (res=16).
MRISapplyReg: Forward Loop (133299)
MRISapplyReg: Dividing by number of hits (133299)
MRISapplyReg: nSrcLost = 38462
4505 points in output label
mris_apply_reg done
On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Try
mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere.left_right rh.sphere
On 10/11/17 5:43 PM, Neuro Lists wrote:
Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help.
I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be.
I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain.
I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register.
I've done:
cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right
I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum:
- mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg
lh.sphere lh.sphere.left_right 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right rh.sphere.left_right --trg rh.lh.source.label
No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped ROIs.
Thanks for your help!
Joe
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.
Sorry, try this
mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
On 10/13/17 2:58 PM, Neuro Lists wrote:
Hi all, I was just wondering if there was any further insight into what I might be doing wrong on this.
Thanks again!
On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists <neuro.mailing.lists@gmail.com mailto:neuro.mailing.lists@gmail.com> wrote:
Hi Doug and Bruce, I forgot to mention that I had tried that as well but without success. As a sanity check, tried flipping a label from the 'bert' subject and it still comes out wrong. I've uploaded a screen shot of the result: https://imgur.com/a/J6Phx Thank you for any input you might have! These were the exact steps the following (I also tried playing around with the options to --streg but without luck): cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right cd ../label mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere $Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $ cwd /home/joe/subjects/bert/label cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere sysname Linux hostname computer machine x86_64 user joe srcvalfile (null) trgvalfile lh_flip.BA45.label nsurfs 2 jac 0 revmap 0 1 Loading ../surf/lh.sphere.left_right 2 Loading ../surf/rh.sphere Loading label lh.BA45.label 4060 points in input label MRISapplyReg: nsurfs = 2, revmap=0, jac=0, hash=1 MRISapplyReg: building hash tables (res=16). MRISapplyReg: Forward Loop (133299) MRISapplyReg: Dividing by number of hits (133299) MRISapplyReg: nSrcLost = 38462 4505 points in output label mris_apply_reg done On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Try mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere.left_right rh.sphere On 10/11/17 5:43 PM, Neuro Lists wrote:Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help. I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be. I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain. I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register. I've done: cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum: 1) mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere lh.sphere.left_right 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right rh.sphere.left_right --trg rh.lh.source.label No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped ROIs. Thanks for your help! Joe _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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> 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, Thanks a lot for looking into it. Unfortunately it's still not working though.
See here: https://imgur.com/a/lxXUH
Thanks again!
On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Sorry, try this
mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
On 10/13/17 2:58 PM, Neuro Lists wrote:
Hi all, I was just wondering if there was any further insight into what I might be doing wrong on this.
Thanks again!
On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists < neuro.mailing.lists@gmail.com> wrote:
Hi Doug and Bruce, I forgot to mention that I had tried that as well but without success. As a sanity check, tried flipping a label from the 'bert' subject and it still comes out wrong. I've uploaded a screen shot of the result:
Thank you for any input you might have!
These were the exact steps the following (I also tried playing around with the options to --streg but without luck):
cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right cd ../label
mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere
$Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $
cwd /home/joe/subjects/bert/label
cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere
sysname Linux
hostname computer
machine x86_64
user joe
srcvalfile (null)
trgvalfile lh_flip.BA45.label
nsurfs 2
jac 0
revmap 0
1 Loading ../surf/lh.sphere.left_right
2 Loading ../surf/rh.sphere
Loading label lh.BA45.label
4060 points in input label
MRISapplyReg: nsurfs = 2, revmap=0, jac=0, hash=1
MRISapplyReg: building hash tables (res=16).
MRISapplyReg: Forward Loop (133299)
MRISapplyReg: Dividing by number of hits (133299)
MRISapplyReg: nSrcLost = 38462
4505 points in output label
mris_apply_reg done
On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Try
mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere.left_right rh.sphere
On 10/11/17 5:43 PM, Neuro Lists wrote:
Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help.
I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be.
I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain.
I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register.
I've done:
cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right
I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum:
- mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg
lh.sphere lh.sphere.left_right 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right rh.sphere.left_right --trg rh.lh.source.label
No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped ROIs.
Thanks for your help!
Joe
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 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.
Is this fsaverage or one of your own subjects?
On 10/17/2017 02:18 PM, Neuro Lists wrote:
Hi Doug, Thanks a lot for looking into it. Unfortunately it's still not working though.
See here: https://imgur.com/a/lxXUH
Thanks again!
On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, try this mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right On 10/13/17 2:58 PM, Neuro Lists wrote:Hi all, I was just wondering if there was any further insight into what I might be doing wrong on this. Thanks again! On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists <neuro.mailing.lists@gmail.com <mailto:neuro.mailing.lists@gmail.com>> wrote: Hi Doug and Bruce, I forgot to mention that I had tried that as well but without success. As a sanity check, tried flipping a label from the 'bert' subject and it still comes out wrong. I've uploaded a screen shot of the result: https://imgur.com/a/J6Phx Thank you for any input you might have! These were the exact steps the following (I also tried playing around with the options to --streg but without luck): cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right cd ../label mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere $Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $ cwd /home/joe/subjects/bert/label cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere sysname Linux hostname computer machine x86_64 user joe srcvalfile (null) trgvalfile lh_flip.BA45.label nsurfs 2 jac 0 revmap 0 1 Loading ../surf/lh.sphere.left_right 2 Loading ../surf/rh.sphere Loading label lh.BA45.label 4060 points in input label MRISapplyReg: nsurfs = 2, revmap=0, jac=0, hash=1 MRISapplyReg: building hash tables (res=16). MRISapplyReg: Forward Loop (133299) MRISapplyReg: Dividing by number of hits (133299) MRISapplyReg: nSrcLost = 38462 4505 points in output label mris_apply_reg done On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Try mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere.left_right rh.sphere On 10/11/17 5:43 PM, Neuro Lists wrote:Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help. I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be. I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain. I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register. I've done: cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum: 1) mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere lh.sphere.left_right 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right rh.sphere.left_right --trg rh.lh.source.label No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped ROIs. Thanks for your help! Joe _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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> 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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> 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.
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Hi, The one I tested with in the last couple of messages is just the standard bert subject after having done:
cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right
And then running:
cd ../label mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
Have I misunderstood something?
Thanks again!
On Tue, Oct 17, 2017 at 4:55 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Is this fsaverage or one of your own subjects?
On 10/17/2017 02:18 PM, Neuro Lists wrote:
Hi Doug, Thanks a lot for looking into it. Unfortunately it's still not working though.
See here: https://imgur.com/a/lxXUH
Thanks again!
On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, try this mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right On 10/13/17 2:58 PM, Neuro Lists wrote:Hi all, I was just wondering if there was any further insight into what I might be doing wrong on this. Thanks again! On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists <neuro.mailing.lists@gmail.com <mailto:neuro.mailing.lists@gmail.com>> wrote: Hi Doug and Bruce, I forgot to mention that I had tried that as well but without success. As a sanity check, tried flipping a label from the 'bert' subject and it still comes out wrong. I've uploaded a screen shot of the result: https://imgur.com/a/J6Phx Thank you for any input you might have! These were the exact steps the following (I also tried playing around with the options to --streg but without luck): cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right cd ../label mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere $Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $ cwd /home/joe/subjects/bert/label cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere sysname Linux hostname computer machine x86_64 user joe srcvalfile (null) trgvalfile lh_flip.BA45.label nsurfs 2 jac 0 revmap 0 1 Loading ../surf/lh.sphere.left_right 2 Loading ../surf/rh.sphere Loading label lh.BA45.label 4060 points in input label MRISapplyReg: nsurfs = 2, revmap=0, jac=0, hash=1 MRISapplyReg: building hash tables (res=16). MRISapplyReg: Forward Loop (133299) MRISapplyReg: Dividing by number of hits (133299) MRISapplyReg: nSrcLost = 38462 4505 points in output label mris_apply_reg done On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Try mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere.left_right rh.sphere On 10/11/17 5:43 PM, Neuro Lists wrote:Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help. I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be. I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain. I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register. I've done: cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum: 1) mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere lh.sphere.left_right 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right rh.sphere.left_right --trg rh.lh.source.label No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped ROIs. Thanks for your help! Joe _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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> 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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>
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.
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
Hi again, I just wanted to revisit this thread to see if I had misunderstood something or had done something incorrectly? The commands I used for bert were as follows:
cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right cd ../label mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
I tried a few different combinations of mris_left_right_register but without luck.
Thanks!
On Tue, Oct 17, 2017 at 11:55 PM, Neuro Lists neuro.mailing.lists@gmail.com wrote:
Hi, The one I tested with in the last couple of messages is just the standard
bert subject after having done:
cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right
rh.sphere.left_right
And then running:
cd ../label mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg
../surf/lh.sphere.left_right ../surf/rh.sphere.left_right
Have I misunderstood something?
Thanks again!
On Tue, Oct 17, 2017 at 4:55 PM, Douglas N Greve <
greve@nmr.mgh.harvard.edu> wrote:
Is this fsaverage or one of your own subjects?
On 10/17/2017 02:18 PM, Neuro Lists wrote:
Hi Doug, Thanks a lot for looking into it. Unfortunately it's still not working though.
See here: https://imgur.com/a/lxXUH
Thanks again!
On Mon, Oct 16, 2017 at 12:31 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Sorry, try this mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere.left_right On 10/13/17 2:58 PM, Neuro Lists wrote:Hi all, I was just wondering if there was any further insight into what I might be doing wrong on this. Thanks again! On Thu, Oct 12, 2017 at 10:30 AM, Neuro Lists <neuro.mailing.lists@gmail.com <mailto:neuro.mailing.lists@gmail.com>> wrote: Hi Doug and Bruce, I forgot to mention that I had tried that as well but without success. As a sanity check, tried flipping a label from the 'bert' subject and it still comes out wrong. I've uploaded a screen shot of the result: https://imgur.com/a/J6Phx Thank you for any input you might have! These were the exact steps the following (I also tried playing around with the options to --streg but without luck): cd ${SUBJECTS_DIR}/bert cd surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right cd ../label mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere $Id: mris_apply_reg.c,v 1.9 2016/12/06 19:40:48 greve Exp $ cwd /home/joe/subjects/bert/label cmdline ../../scripts/mris_apply_reg --src-label lh.BA45.label --trg lh_flip.BA45.label --streg ../surf/lh.sphere.left_right ../surf/rh.sphere sysname Linux hostname computer machine x86_64 user joe srcvalfile (null) trgvalfile lh_flip.BA45.label nsurfs 2 jac 0 revmap 0 1 Loading ../surf/lh.sphere.left_right 2 Loading ../surf/rh.sphere Loading label lh.BA45.label 4060 points in input label MRISapplyReg: nsurfs = 2, revmap=0, jac=0, hash=1 MRISapplyReg: building hash tables (res=16). MRISapplyReg: Forward Loop (133299) MRISapplyReg: Dividing by number of hits (133299) MRISapplyReg: nSrcLost = 38462 4505 points in output label mris_apply_reg done On Thu, Oct 12, 2017 at 5:06 AM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Try mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere.left_right rh.sphere On 10/11/17 5:43 PM, Neuro Lists wrote:Hi all, I've searched the lists extensively and have not been able to resolve my problem. I'd greatly appreciated any help. I have run the recon-all pipeline on a number of subjects, made the appropriate fixes and am happy with the surfaces. For each subject, I have a number of ROIs that are created programmatically and they are exactly as they should be. These ROIs are on the "regular" surfaces, not the inflated ones. In other words, opening the brainmask.mgz in freeview and just loading the label file results in the ROI being where I expect it to be. I'm now trying to flip the ROI onto the contralateral hemisphere and this is going terribly wrong. No matter what I try, the ROI ends up being generated far outside of the brain. I was originally trying to use the xhemi pipeline, but then I realized from the forums that I could just use mris_left_right_register. I've done: cd subject/surf mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right I've then tried using a number of varieties of mri_apply_reg that have been listed on the forum: 1) mris_apply_reg --src-label your.lh.label --trg your.rh.label -streg lh.sphere lh.sphere.left_right 2) mris_apply_reg --src-label lh.source.label --streg lh.sphere.left_right rh.sphere.left_right --trg rh.lh.source.label No matter what I try though, the flipped ROI ends up being way outside of the brain when I overlay it on the brainmask. Is this because the flipped ROI should instead be visualized on the inflated hemisphere? If so, how can I get it to overlay properly onto the brainmask so that I can be sure it's correct? My ultimate goal is to get anatomical stats from the original and flipped
ROIs.
Thanks for your help! Joe _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E
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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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>
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.
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
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Neuro Lists