Hello everyone,
We used tksurfer to draw a specific region on the left hemisphere of fsaverage subject and we would like to automatically register the label from the left hemisphere to the right hemisphere.
Since FreeSurfer provides tools to compute a symmetric fsaverage ( https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I was wondering if there was any command to have the manually drawn label on the left hemisphere to the right hemisphere.
Thanks in advance for your help. Alexandre
You can use mris_left_right_register, then use mris_apply_reg with the --src-label option. I can't remember whether these are in 5.3 (or whether 5.3 has the --src-label), so let me know if you need updates
On 04/28/2016 09:06 AM, Alexandre Routier wrote:
Hello everyone,
We used tksurfer to draw a specific region on the left hemisphere of fsaverage subject and we would like to automatically register the label from the left hemisphere to the right hemisphere.
Since FreeSurfer provides tools to compute a symmetric fsaverage (https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I was wondering if there was any command to have the manually drawn label on the left hemisphere to the right hemisphere.
Thanks in advance for your help. Alexandre
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Douglas,
Unfortunately, I didn't find the command mris_apply_reg in FreeSurfer 5.3. Is there anything to do to solve this problem ?
Alex
2016-04-28 18:15 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
You can use mris_left_right_register, then use mris_apply_reg with the --src-label option. I can't remember whether these are in 5.3 (or whether 5.3 has the --src-label), so let me know if you need updates
On 04/28/2016 09:06 AM, Alexandre Routier wrote:
Hello everyone,
We used tksurfer to draw a specific region on the left hemisphere of fsaverage subject and we would like to automatically register the label from the left hemisphere to the right hemisphere.
Since FreeSurfer provides tools to compute a symmetric fsaverage (https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I was wondering if there was any command to have the manually drawn label on the left hemisphere to the right hemisphere.
Thanks in advance for your help. Alexandre
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/
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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.
ive put a copy here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg
On 05/03/2016 04:21 AM, Alexandre Routier wrote:
Hello Douglas,
Unfortunately, I didn't find the command mris_apply_reg in FreeSurfer 5.3. Is there anything to do to solve this problem ?
Alex
2016-04-28 18:15 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
You can use mris_left_right_register, then use mris_apply_reg with the --src-label option. I can't remember whether these are in 5.3 (or whether 5.3 has the --src-label), so let me know if you need updates On 04/28/2016 09:06 AM, Alexandre Routier wrote: > Hello everyone, > > We used tksurfer to draw a specific region on the left hemisphere of > fsaverage subject and we would like to automatically register the > label from the left hemisphere to the right hemisphere. > > Since FreeSurfer provides tools to compute a symmetric fsaverage > (https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I was wondering if > there was any command to have the manually drawn label on the left > hemisphere to the right hemisphere. > > Thanks in advance for your help. > Alexandre > > > _______________________________________________ > 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 Fax: 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
Hello,
Sorry for my late reply but I just tried these commands today. In fact, I don't have mris_left_right_register on Freesurfer 5.3 so I used this one : https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/ and it seems to work.
Concerning mris_apply_reg, I am not sure how to use it. 1) My custom label is on fsaverage. I use the command: mri_label2label --srcsubject fsaverage --srclabel fsaverage/lh.manual_label.label --trgsubject IdSubject --trglabel IdSubject/lh.manual_label.label --hemi lh --regmethod surface to come back to the native space
2) mris_left_right_register enables me to have symetric hemispheres on the subject
3) Then I want to correspond my label (defined on left hemisphere) to the right hemisphere. I specify IdSubject/lh.manual_label.label for the --src-label flag but the output flag, is " --streg lh.sphere rh.sphere.left_right" correct ? I can choose between "--trg trgvalfile" and "--streg srcreg1 trgreg1 " but I don't know what is the difference and how to use it.
(To be sure, do I need to use one on these following flags: --jac : use jacobian correction --no-rev : do not do reverse mapping --randn : replace input with WGN --ones : replace input with ones ?)
Alexandre
2016-05-04 21:07 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
ive put a copy here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg
On 05/03/2016 04:21 AM, Alexandre Routier wrote:
Hello Douglas,
Unfortunately, I didn't find the command mris_apply_reg in FreeSurfer 5.3. Is there anything to do to solve this problem ?
Alex
2016-04-28 18:15 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
You can use mris_left_right_register, then use mris_apply_reg withthe
--src-label option. I can't remember whether these are in 5.3 (or whether 5.3 has the --src-label), so let me know if you need updates On 04/28/2016 09:06 AM, Alexandre Routier wrote: > Hello everyone, > > We used tksurfer to draw a specific region on the left hemisphereof
> fsaverage subject and we would like to automatically register the > label from the left hemisphere to the right hemisphere. > > Since FreeSurfer provides tools to compute a symmetric fsaverage > (https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I was wondering if > there was any command to have the manually drawn label on the left > hemisphere to the right hemisphere. > > Thanks in advance for your help. > Alexandre > > > _______________________________________________ > 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 Fax: 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
-- 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
Quick update on my situation: it turns out that I have a problem corresponding to the source label: ERROR: Option --src-label unknown
Thanks in advance for your help :)
2016-06-09 20:08 GMT+02:00 Alexandre Routier alexandre.routier@gmail.com:
Hello,
Sorry for my late reply but I just tried these commands today. In fact, I don't have mris_left_right_register on Freesurfer 5.3 so I used this one : https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/ and it seems to work.
Concerning mris_apply_reg, I am not sure how to use it.
- My custom label is on fsaverage. I use the command:
mri_label2label --srcsubject fsaverage --srclabel fsaverage/lh.manual_label.label --trgsubject IdSubject --trglabel IdSubject/lh.manual_label.label --hemi lh --regmethod surface to come back to the native space
- mris_left_right_register enables me to have symetric hemispheres on
the subject
- Then I want to correspond my label (defined on left hemisphere) to the
right hemisphere. I specify IdSubject/lh.manual_label.label for the --src-label flag but the output flag, is " --streg lh.sphere rh.sphere.left_right" correct ? I can choose between "--trg trgvalfile" and "--streg srcreg1 trgreg1 " but I don't know what is the difference and how to use it.
(To be sure, do I need to use one on these following flags: --jac : use jacobian correction --no-rev : do not do reverse mapping --randn : replace input with WGN --ones : replace input with ones ?)
Alexandre
2016-05-04 21:07 GMT+02:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
ive put a copy here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_apply_reg
On 05/03/2016 04:21 AM, Alexandre Routier wrote:
Hello Douglas,
Unfortunately, I didn't find the command mris_apply_reg in FreeSurfer 5.3. Is there anything to do to solve this problem ?
Alex
2016-04-28 18:15 GMT+02:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
You can use mris_left_right_register, then use mris_apply_reg withthe
--src-label option. I can't remember whether these are in 5.3 (or whether 5.3 has the --src-label), so let me know if you need updates On 04/28/2016 09:06 AM, Alexandre Routier wrote: > Hello everyone, > > We used tksurfer to draw a specific region on the left hemisphereof
> fsaverage subject and we would like to automatically register the > label from the left hemisphere to the right hemisphere. > > Since FreeSurfer provides tools to compute a symmetric fsaverage > (https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi), I was wondering if > there was any command to have the manually drawn label on the left > hemisphere to the right hemisphere. > > Thanks in advance for your help. > Alexandre > > > _______________________________________________ > 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 Fax: 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
-- 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
-
Alexandre Routier -
Douglas N Greve