Hi All,
My question is about using mri_label2label. When mapping the labels from one subject to another the number of vertices of each ROI is different. Is that something to be expected?
How much of a difference does a number of vertices of 50 compare to 40 have on measures like thickness, grey matter and surface area?
I would really appreciate some help
Thank you,
Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada
Hi Daiana
yes, that is to be expected given the nonlinear nature of the cross-subject registration. It shouldn't bias things, although you'll need to give us more details if you want a more definitive answer.
cheers Bruce
On Mon, 24 Oct 2016, Daya P wrote:
Hi All,
My question is about using mri_label2label. When mapping the labels from one subject to another the number of vertices of each ROI is different. Is that something to be expected?
How much of a difference does a number of vertices of 50 compare to 40 have on measures like thickness, grey matter and surface area?
I would really appreciate some help
Thank you,
Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada
Hi Bruce,
I drew ROIs on an initial subject and then after registering all other subjects to the initial one, used mri_label2label to map the ROIs from the initial subject to subsequent ones. I am interested in looking at asymmetry between left and right regions.
I had two concerns, one that the ROIs have different # vertices on different subjects, but as you mentioned the nonlinear process makes sense, since each subject does not have the exact same brain size and curvature.
Another concern was that the ROIs on the left and right hemisphere in a subject do not have the exact same number of vertices. Would a difference of 10 vertices max bias results?
Thank you for your help,
Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada
On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Daiana
yes, that is to be expected given the nonlinear nature of the cross-subject registration. It shouldn't bias things, although you'll need to give us more details if you want a more definitive answer.
cheers Bruce
On Mon, 24 Oct 2016, Daya P wrote:
Hi All,
My question is about using mri_label2label. When mapping the labels from one subject to another the number of vertices of each ROI is different. Is that something to be expected?
How much of a difference does a number of vertices of 50 compare to 40 have on measures like thickness, grey matter and surface area?
I would really appreciate some help
Thank you,
Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada
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.
It would depend on how big the ROI is to begin with. Do you know that we have our own interhemispheric analysis that might be better for this? Check out
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 10/24/2016 12:33 PM, Daya P wrote:
Hi Bruce,
I drew ROIs on an initial subject and then after registering all other subjects to the initial one, used mri_label2label to map the ROIs from the initial subject to subsequent ones. I am interested in looking at asymmetry between left and right regions.
I had two concerns, one that the ROIs have different # vertices on different subjects, but as you mentioned the nonlinear process makes sense, since each subject does not have the exact same brain size and curvature.
Another concern was that the ROIs on the left and right hemisphere in a subject do not have the exact same number of vertices. Would a difference of 10 vertices max bias results?
Thank you for your help,
Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada
On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daiana yes, that is to be expected given the nonlinear nature of the cross-subject registration. It shouldn't bias things, although you'll need to give us more details if you want a more definitive answer. cheers Bruce On Mon, 24 Oct 2016, Daya P wrote: Hi All, My question is about using mri_label2label. When mapping the labels from one subject to another the number of vertices of each ROI is different. Is that something to be expected? How much of a difference does a number of vertices of 50 compare to 40 have on measures like thickness, grey matter and surface area? I would really appreciate some help Thank you, Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada _______________________________________________ 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
Thank you for your help!
I created a registration template and atlas from scratch could I input that in the interhemispheric registration analysis?
The ROIs for the diffrerent regions per hemisphere are 50-100 vertices On Oct 24, 2016 5:03 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It would depend on how big the ROI is to begin with. Do you know that we have our own interhemispheric analysis that might be better for this? Check out
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 10/24/2016 12:33 PM, Daya P wrote:
Hi Bruce,
I drew ROIs on an initial subject and then after registering all other subjects to the initial one, used mri_label2label to map the ROIs from the initial subject to subsequent ones. I am interested in looking at asymmetry between left and right regions.
I had two concerns, one that the ROIs have different # vertices on different subjects, but as you mentioned the nonlinear process makes sense, since each subject does not have the exact same brain size and curvature.
Another concern was that the ROIs on the left and right hemisphere in a subject do not have the exact same number of vertices. Would a difference of 10 vertices max bias results?
Thank you for your help,
Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada
On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daiana yes, that is to be expected given the nonlinear nature of the cross-subject registration. It shouldn't bias things, although you'll need to give us more details if you want a more definitive answer. cheers Bruce On Mon, 24 Oct 2016, Daya P wrote: Hi All, My question is about using mri_label2label. When mapping the labels from one subject to another the number of vertices of each ROI is different. Is that something to be expected? How much of a difference does a number of vertices of 50 compare to 40 have on measures like thickness, grey matter and surface area? I would really appreciate some help Thank you, Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada _______________________________________________ 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
A difference of 10 out of 500 or 1000 does not both me at all. Why do you need to create your own atlas? It is doable for the cross hemi stuff, it is just difficult.
On 10/26/16 10:16 AM, Daya P wrote:
Thank you for your help!
I created a registration template and atlas from scratch could I input that in the interhemispheric registration analysis?
The ROIs for the diffrerent regions per hemisphere are 50-100 vertices
On Oct 24, 2016 5:03 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It would depend on how big the ROI is to begin with. Do you know that we have our own interhemispheric analysis that might be better for this? Check out http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> On 10/24/2016 12:33 PM, Daya P wrote: > Hi Bruce, > > I drew ROIs on an initial subject and then after registering all other > subjects to the initial one, used mri_label2label to map the ROIs from > the initial subject to subsequent ones. > I am interested in looking at asymmetry between left and right regions. > > I had two concerns, one that the ROIs have different # vertices on > different subjects, but as you mentioned the nonlinear process makes > sense, since each subject does not have the exact same brain size and > curvature. > > Another concern was that the ROIs on the left and right hemisphere in > a subject do not have the exact same number of vertices. Would a > difference of 10 vertices max bias results? > > Thank you for your help, > > Daiana R. Pur > Research Assistant > Canadian Surgical Technologies & Advanced Robotics > Brain and Mind Institute > Western University > London, ON, N6A 5B7 > Canada > > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi Daiana > > yes, that is to be expected given the nonlinear nature of the > cross-subject registration. It shouldn't bias things, although > you'll need to give us more details if you want a more definitive > answer. > > cheers > Bruce > > > > On Mon, 24 Oct 2016, Daya P wrote: > > Hi All, > > My question is about using mri_label2label. When mapping the > labels from one > subject to another the number of vertices of each ROI is > different. Is that > something to be expected? > > How much of a difference does a number of vertices of 50 > compare to 40 have > on measures like thickness, grey matter and surface area? > > I would really appreciate some help > > Thank you, > > Daiana R. Pur > Research Assistant > Canadian Surgical Technologies & Advanced Robotics > Brain and Mind Institute > Western University > London, ON, N6A 5B7 > Canada > > > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <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> -- 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 <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/ <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 <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 Doug,
I needed to make a registration template and an cortical atlas because I am trying to measure cortical thickness, GM and surface area on cat brains.
What would be the necessary changes? Would it be possible (and appropriate) to use just mris_left_right_register instead?
Daiana
On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
A difference of 10 out of 500 or 1000 does not both me at all. Why do you need to create your own atlas? It is doable for the cross hemi stuff, it is just difficult.
On 10/26/16 10:16 AM, Daya P wrote:
Thank you for your help!
I created a registration template and atlas from scratch could I input that in the interhemispheric registration analysis?
The ROIs for the diffrerent regions per hemisphere are 50-100 vertices On Oct 24, 2016 5:03 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
It would depend on how big the ROI is to begin with. Do you know that we have our own interhemispheric analysis that might be better for this? Check out
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 10/24/2016 12:33 PM, Daya P wrote:
Hi Bruce,
I drew ROIs on an initial subject and then after registering all other subjects to the initial one, used mri_label2label to map the ROIs from the initial subject to subsequent ones. I am interested in looking at asymmetry between left and right regions.
I had two concerns, one that the ROIs have different # vertices on different subjects, but as you mentioned the nonlinear process makes sense, since each subject does not have the exact same brain size and curvature.
Another concern was that the ROIs on the left and right hemisphere in a subject do not have the exact same number of vertices. Would a difference of 10 vertices max bias results?
Thank you for your help,
Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada
On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Daiana yes, that is to be expected given the nonlinear nature of the cross-subject registration. It shouldn't bias things, although you'll need to give us more details if you want a more definitive answer. cheers Bruce On Mon, 24 Oct 2016, Daya P wrote: Hi All, My question is about using mri_label2label. When mapping the labels from one subject to another the number of vertices of each ROI is different. Is that something to be expected? How much of a difference does a number of vertices of 50 compare to 40 have on measures like thickness, grey matter and surface area? I would really appreciate some help Thank you, Daiana R. Pur Research Assistant Canadian Surgical Technologies & Advanced Robotics Brain and Mind Institute Western University London, ON, N6A 5B7 Canada _______________________________________________ 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 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.
I've written a script that will come out with version 6, but I've put it here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
I think it should work in 5.3, but I'm not sure. If not, you can download the dev version and make the atlas using that. Run it with --help to get info on how to run it.
On 10/28/2016 05:10 PM, Daya P wrote:
Hi Doug,
I needed to make a registration template and an cortical atlas because I am trying to measure cortical thickness, GM and surface area on cat brains.
What would be the necessary changes? Would it be possible (and appropriate) to use just mris_left_right_register instead?
Daiana
On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
A difference of 10 out of 500 or 1000 does not both me at all. Why do you need to create your own atlas? It is doable for the cross hemi stuff, it is just difficult. On 10/26/16 10:16 AM, Daya P wrote:Thank you for your help! I created a registration template and atlas from scratch could I input that in the interhemispheric registration analysis? The ROIs for the diffrerent regions per hemisphere are 50-100 vertices On Oct 24, 2016 5:03 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: It would depend on how big the ROI is to begin with. Do you know that we have our own interhemispheric analysis that might be better for this? Check out http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> On 10/24/2016 12:33 PM, Daya P wrote: > Hi Bruce, > > I drew ROIs on an initial subject and then after registering all other > subjects to the initial one, used mri_label2label to map the ROIs from > the initial subject to subsequent ones. > I am interested in looking at asymmetry between left and right regions. > > I had two concerns, one that the ROIs have different # vertices on > different subjects, but as you mentioned the nonlinear process makes > sense, since each subject does not have the exact same brain size and > curvature. > > Another concern was that the ROIs on the left and right hemisphere in > a subject do not have the exact same number of vertices. Would a > difference of 10 vertices max bias results? > > Thank you for your help, > > Daiana R. Pur > Research Assistant > Canadian Surgical Technologies & Advanced Robotics > Brain and Mind Institute > Western University > London, ON, N6A 5B7 > Canada > > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi Daiana > > yes, that is to be expected given the nonlinear nature of the > cross-subject registration. It shouldn't bias things, although > you'll need to give us more details if you want a more definitive > answer. > > cheers > Bruce > > > > On Mon, 24 Oct 2016, Daya P wrote: > > Hi All, > > My question is about using mri_label2label. When mapping the > labels from one > subject to another the number of vertices of each ROI is > different. Is that > something to be expected? > > How much of a difference does a number of vertices of 50 > compare to 40 have > on measures like thickness, grey matter and surface area? > > I would really appreciate some help > > Thank you, > > Daiana R. Pur > Research Assistant > Canadian Surgical Technologies & Advanced Robotics > Brain and Mind Institute > Western University > London, ON, N6A 5B7 > Canada > > > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <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> -- 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 <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/ <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 <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>_______________________________________________ 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
Thank you a lot!
I will try this. I had another question regarding statistical analysis for asymmetry. I have seen several papers that take the measures that come from freesurfer (i.e. cortical thickness of auditory cortex), and use MATLAB or SPSS to run statistical tests.
I am looking at 13 regions in each hemisphere and want to check for asymmetry across 9 participants. Is there a way to do this within Freesurfer? Otherwise, I am still looking into what the most appropriate test and post hoc test would be. From asking several people there doesn't seem to be a straight answer.
Thank you, Daiana
On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I've written a script that will come out with version 6, but I've put it here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
I think it should work in 5.3, but I'm not sure. If not, you can download the dev version and make the atlas using that. Run it with --help to get info on how to run it.
On 10/28/2016 05:10 PM, Daya P wrote:
Hi Doug,
I needed to make a registration template and an cortical atlas because I am trying to measure cortical thickness, GM and surface area on cat brains.
What would be the necessary changes? Would it be possible (and appropriate) to use just mris_left_right_register instead?
Daiana
On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
A difference of 10 out of 500 or 1000 does not both me at all. Why do you need to create your own atlas? It is doable for the cross hemi stuff, it is just difficult. On 10/26/16 10:16 AM, Daya P wrote:Thank you for your help! I created a registration template and atlas from scratch could I input that in the interhemispheric registration analysis? The ROIs for the diffrerent regions per hemisphere are 50-100 vertices On Oct 24, 2016 5:03 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>wrote:
It would depend on how big the ROI is to begin with. Do you know that we have our own interhemispheric analysis that might be better for this? Check out http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> On 10/24/2016 12:33 PM, Daya P wrote: > Hi Bruce, > > I drew ROIs on an initial subject and then after registering all other > subjects to the initial one, used mri_label2label to map the ROIs from > the initial subject to subsequent ones. > I am interested in looking at asymmetry between left and right regions. > > I had two concerns, one that the ROIs have different # vertices on > different subjects, but as you mentioned the nonlinear process makes > sense, since each subject does not have the exact same brain size and > curvature. > > Another concern was that the ROIs on the left and right hemisphere in > a subject do not have the exact same number of vertices. Would a > difference of 10 vertices max bias results? > > Thank you for your help, > > Daiana R. Pur > Research Assistant > Canadian Surgical Technologies & Advanced Robotics > Brain and Mind Institute > Western University > London, ON, N6A 5B7 > Canada > > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi Daiana > > yes, that is to be expected given the nonlinear nature of the > cross-subject registration. It shouldn't bias things, although > you'll need to give us more details if you want a more definitive > answer. > > cheers > Bruce > > > > On Mon, 24 Oct 2016, Daya P wrote: > > Hi All, > > My question is about using mri_label2label. When mapping the > labels from one > subject to another the number of vertices of each ROI is > different. Is that > something to be expected? > > How much of a difference does a number of vertices of 50 > compare to 40 have > on measures like thickness, grey matter and surface area? > > I would really appreciate some help > > Thank you, > > Daiana R. Pur > Research Assistant > Canadian Surgical Technologies & Advanced Robotics > Brain and Mind Institute > Western University > London, ON, N6A 5B7 > Canada > > > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <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> -- 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 <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/ <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 <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>_______________________________________________ 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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-- 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
You can certainly get the lh and rh ROI stats in table form and then do an asymmetry analysis. Or you can use the xhemi stream to do a vertex-wise analysis. the difference is the difference between ROI and map-based analysis
On 11/01/2016 03:47 PM, Daya P wrote:
Thank you a lot!
I will try this. I had another question regarding statistical analysis for asymmetry. I have seen several papers that take the measures that come from freesurfer (i.e. cortical thickness of auditory cortex), and use MATLAB or SPSS to run statistical tests.
I am looking at 13 regions in each hemisphere and want to check for asymmetry across 9 participants. Is there a way to do this within Freesurfer? Otherwise, I am still looking into what the most appropriate test and post hoc test would be. From asking several people there doesn't seem to be a straight answer.
Thank you, Daiana
On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I've written a script that will come out with version 6, but I've put it here https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas <https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas> I think it should work in 5.3, but I'm not sure. If not, you can download the dev version and make the atlas using that. Run it with --help to get info on how to run it. On 10/28/2016 05:10 PM, Daya P wrote: > Hi Doug, > > I needed to make a registration template and an cortical atlas because > I am trying to measure cortical thickness, GM and surface area on cat > brains. > > What would be the necessary changes? > Would it be possible (and appropriate) to use just > mris_left_right_register instead? > > Daiana > > On Fri, Oct 28, 2016 at 11:34 AM, 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: > > A difference of 10 out of 500 or 1000 does not both me at all. Why > do you need to create your own atlas? It is doable for the cross > hemi stuff, it is just difficult. > > > On 10/26/16 10:16 AM, Daya P wrote: >> >> Thank you for your help! >> >> I created a registration template and atlas from scratch could I >> input that in the interhemispheric registration analysis? >> >> The ROIs for the diffrerent regions per hemisphere are 50-100 >> vertices >> >> On Oct 24, 2016 5:03 PM, "Douglas N 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: >> >> It would depend on how big the ROI is to begin with. Do you >> know that we >> have our own interhemispheric analysis that might be better >> for this? >> Check out >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>> >> >> >> On 10/24/2016 12:33 PM, Daya P wrote: >> > Hi Bruce, >> > >> > I drew ROIs on an initial subject and then after >> registering all other >> > subjects to the initial one, used mri_label2label to map >> the ROIs from >> > the initial subject to subsequent ones. >> > I am interested in looking at asymmetry between left and >> right regions. >> > >> > I had two concerns, one that the ROIs have different # >> vertices on >> > different subjects, but as you mentioned the nonlinear >> process makes >> > sense, since each subject does not have the exact same >> brain size and >> > curvature. >> > >> > Another concern was that the ROIs on the left and right >> hemisphere in >> > a subject do not have the exact same number of vertices. >> Would a >> > difference of 10 vertices max bias results? >> > >> > Thank you for your help, >> > >> > Daiana R. Pur >> > Research Assistant >> > Canadian Surgical Technologies & Advanced Robotics >> > Brain and Mind Institute >> > Western University >> > London, ON, N6A 5B7 >> > Canada >> > >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: >> > >> > Hi Daiana >> > >> > yes, that is to be expected given the nonlinear nature >> of the >> > cross-subject registration. It shouldn't bias things, >> although >> > you'll need to give us more details if you want a more >> definitive >> > answer. >> > >> > cheers >> > Bruce >> > >> > >> > >> > On Mon, 24 Oct 2016, Daya P wrote: >> > >> > Hi All, >> > >> > My question is about using mri_label2label. When >> mapping the >> > labels from one >> > subject to another the number of vertices of each >> ROI is >> > different. Is that >> > something to be expected? >> > >> > How much of a difference does a number of vertices >> of 50 >> > compare to 40 have >> > on measures like thickness, grey matter and surface >> area? >> > >> > I would really appreciate some help >> > >> > Thank you, >> > >> > Daiana R. Pur >> > Research Assistant >> > Canadian Surgical Technologies & Advanced Robotics >> > Brain and Mind Institute >> > Western University >> > London, ON, N6A 5B7 >> > Canada >> > >> > >> > >> > _______________________________________________ >> > 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>> >> <mailto: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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <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> >> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> >> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> >> <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> >> <mailto: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> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel: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: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> >> <https://gate.nmr.mgh.harvard.edu/filedrop2 <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> >> <http://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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> >> >> _______________________________________________ >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <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> >> <mailto: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> >> <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> > <mailto: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> > <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> > <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> -- 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 <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/ <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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
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Hi,
I have gotten the lh and rh ROIs stats with mris_anatomical_stats before, is there any statistical tests in particular that you recommend for asymmetry? What I have done is a two-way anova and paired t-test with Bonferroni correction. Would like to hear your opinion on that.
Also, I would be interested in the vertex-wise analysis, I will look into that. How can I do the xhemi analysis after make_folding_atlas?
Thank you! Daiana
On Tue, Nov 1, 2016 at 5:22 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You can certainly get the lh and rh ROI stats in table form and then do an asymmetry analysis. Or you can use the xhemi stream to do a vertex-wise analysis. the difference is the difference between ROI and map-based analysis
On 11/01/2016 03:47 PM, Daya P wrote:
Thank you a lot!
I will try this. I had another question regarding statistical analysis for asymmetry. I have seen several papers that take the measures that come from freesurfer (i.e. cortical thickness of auditory cortex), and use MATLAB or SPSS to run statistical tests.
I am looking at 13 regions in each hemisphere and want to check for asymmetry across 9 participants. Is there a way to do this within Freesurfer? Otherwise, I am still looking into what the most appropriate test and post hoc test would be. From asking several people there doesn't seem to be a straight answer.
Thank you, Daiana
On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I've written a script that will come out with version 6, but I've put it here https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas <https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas I think it should work in 5.3, but I'm not sure. If not, you can download the dev version and make the atlas using that. Run it with --help to get info on how to run it. On 10/28/2016 05:10 PM, Daya P wrote: > Hi Doug, > > I needed to make a registration template and an cortical atlas because > I am trying to measure cortical thickness, GM and surface area on cat > brains. > > What would be the necessary changes? > Would it be possible (and appropriate) to use just > mris_left_right_register instead? > > Daiana > > On Fri, Oct 28, 2016 at 11:34 AM, 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: > > A difference of 10 out of 500 or 1000 does not both me at all. Why > do you need to create your own atlas? It is doable for thecross
> hemi stuff, it is just difficult. > > > On 10/26/16 10:16 AM, Daya P wrote: >> >> Thank you for your help! >> >> I created a registration template and atlas from scratch could I >> input that in the interhemispheric registration analysis? >> >> The ROIs for the diffrerent regions per hemisphere are 50-100 >> vertices >> >> On Oct 24, 2016 5:03 PM, "Douglas N 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: >> >> It would depend on how big the ROI is to begin with. Doyou
>> know that we >> have our own interhemispheric analysis that might bebetter
>> for this? >> Check out >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>> >> >> >> On 10/24/2016 12:33 PM, Daya P wrote: >> > Hi Bruce, >> > >> > I drew ROIs on an initial subject and then after >> registering all other >> > subjects to the initial one, used mri_label2label to map >> the ROIs from >> > the initial subject to subsequent ones. >> > I am interested in looking at asymmetry between left and >> right regions. >> > >> > I had two concerns, one that the ROIs have different # >> vertices on >> > different subjects, but as you mentioned the nonlinear >> process makes >> > sense, since each subject does not have the exact same >> brain size and >> > curvature. >> > >> > Another concern was that the ROIs on the left and right >> hemisphere in >> > a subject do not have the exact same number of vertices. >> Would a >> > difference of 10 vertices max bias results? >> > >> > Thank you for your help, >> > >> > Daiana R. Pur >> > Research Assistant >> > Canadian Surgical Technologies & Advanced Robotics >> > Brain and Mind Institute >> > Western University >> > London, ON, N6A 5B7 >> > Canada >> > >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: >> > >> > Hi Daiana >> > >> > yes, that is to be expected given the nonlinear nature >> of the >> > cross-subject registration. It shouldn't biasthings,
>> although >> > you'll need to give us more details if you want a more >> definitive >> > answer. >> > >> > cheers >> > Bruce >> > >> > >> > >> > On Mon, 24 Oct 2016, Daya P wrote: >> > >> > Hi All, >> > >> > My question is about using mri_label2label. When >> mapping the >> > labels from one >> > subject to another the number of vertices ofeach
>> ROI is >> > different. Is that >> > something to be expected? >> > >> > How much of a difference does a number of vertices >> of 50 >> > compare to 40 have >> > on measures like thickness, grey matter and surface >> area? >> > >> > I would really appreciate some help >> > >> > Thank you, >> > >> > Daiana R. Pur >> > Research Assistant >> > Canadian Surgical Technologies & Advanced Robotics >> > Brain and Mind Institute >> > Western University >> > London, ON, N6A 5B7 >> > Canada >> > >> > >> > >> > _______________________________________________ >> > 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>> >> <mailto: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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <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 toyou
>> 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> >> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> >> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> >> <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> >> <mailto: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> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel: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: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> >> <https://gate.nmr.mgh.harvard.edu/filedrop2 <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> >> <http://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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> >> >> _______________________________________________ >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <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> >> <mailto: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> >> <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> > <mailto: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> > <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> > <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
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On 11/01/2016 05:58 PM, Daya P wrote:
Hi,
I have gotten the lh and rh ROIs stats with mris_anatomical_stats before, is there any statistical tests in particular that you recommend for asymmetry? What I have done is a two-way anova and paired t-test with Bonferroni correction. Would like to hear your opinion on that.
That sounds about right. A lot of people will do a laterality index (L-R)/(L+R)
Also, I would be interested in the vertex-wise analysis, I will look into that. How can I do the xhemi analysis after make_folding_atlas?
Just follow the instructions on the xhemi page
Thank you! Daiana
On Tue, Nov 1, 2016 at 5:22 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
You can certainly get the lh and rh ROI stats in table form and then do an asymmetry analysis. Or you can use the xhemi stream to do a vertex-wise analysis. the difference is the difference between ROI and map-based analysis On 11/01/2016 03:47 PM, Daya P wrote: > Thank you a lot! > > I will try this. I had another question regarding statistical analysis > for asymmetry. I have seen several papers that take the measures that > come from freesurfer (i.e. cortical thickness of auditory cortex), and > use MATLAB or SPSS to run statistical tests. > > I am looking at 13 regions in each hemisphere and want to check for > asymmetry across 9 participants. Is there a way to do this within > Freesurfer? > Otherwise, I am still looking into what the most appropriate test and > post hoc test would be. From asking several people there doesn't seem > to be a straight answer. > > Thank you, > Daiana > > On Tue, Nov 1, 2016 at 12:51 PM, Douglas N 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've written a script that will come out with version 6, but I've > put it > here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas <https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas> > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas <https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas>> > > I think it should work in 5.3, but I'm not sure. If not, you can > download the dev version and make the atlas using that. Run it with > --help to get info on how to run it. > > > > On 10/28/2016 05:10 PM, Daya P wrote: > > Hi Doug, > > > > I needed to make a registration template and an cortical atlas > because > > I am trying to measure cortical thickness, GM and surface area > on cat > > brains. > > > > What would be the necessary changes? > > Would it be possible (and appropriate) to use just > > mris_left_right_register instead? > > > > Daiana > > > > On Fri, Oct 28, 2016 at 11:34 AM, 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>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > A difference of 10 out of 500 or 1000 does not both me at > all. Why > > do you need to create your own atlas? It is doable for the cross > > hemi stuff, it is just difficult. > > > > > > On 10/26/16 10:16 AM, Daya P wrote: > >> > >> Thank you for your help! > >> > >> I created a registration template and atlas from scratch > could I > >> input that in the interhemispheric registration analysis? > >> > >> The ROIs for the diffrerent regions per hemisphere are 50-100 > >> vertices > >> > >> On Oct 24, 2016 5:03 PM, "Douglas N Greve" > >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > >> > >> It would depend on how big the ROI is to begin with. Do you > >> know that we > >> have our own interhemispheric analysis that might be better > >> for this? > >> Check out > >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> > <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>> > >> <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> > <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>>> > >> > >> > >> On 10/24/2016 12:33 PM, Daya P wrote: > >> > Hi Bruce, > >> > > >> > I drew ROIs on an initial subject and then after > >> registering all other > >> > subjects to the initial one, used mri_label2label to map > >> the ROIs from > >> > the initial subject to subsequent ones. > >> > I am interested in looking at asymmetry between left and > >> right regions. > >> > > >> > I had two concerns, one that the ROIs have different # > >> vertices on > >> > different subjects, but as you mentioned the nonlinear > >> process makes > >> > sense, since each subject does not have the exact same > >> brain size and > >> > curvature. > >> > > >> > Another concern was that the ROIs on the left and right > >> hemisphere in > >> > a subject do not have the exact same number of vertices. > >> Would a > >> > difference of 10 vertices max bias results? > >> > > >> > Thank you for your help, > >> > > >> > Daiana R. Pur > >> > Research Assistant > >> > Canadian Surgical Technologies & Advanced Robotics > >> > Brain and Mind Institute > >> > Western University > >> > London, ON, N6A 5B7 > >> > Canada > >> > > >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl > >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>> wrote: > >> > > >> > Hi Daiana > >> > > >> > yes, that is to be expected given the nonlinear > nature > >> of the > >> > cross-subject registration. It shouldn't bias things, > >> although > >> > you'll need to give us more details if you want a > more > >> definitive > >> > answer. > >> > > >> > cheers > >> > Bruce > >> > > >> > > >> > > >> > On Mon, 24 Oct 2016, Daya P wrote: > >> > > >> > Hi All, > >> > > >> > My question is about using mri_label2label. When > >> mapping the > >> > labels from one > >> > subject to another the number of vertices of each > >> ROI is > >> > different. Is that > >> > something to be expected? > >> > > >> > How much of a difference does a number of > vertices > >> of 50 > >> > compare to 40 have > >> > on measures like thickness, grey matter and > surface > >> area? > >> > > >> > I would really appreciate some help > >> > > >> > Thank you, > >> > > >> > Daiana R. Pur > >> > Research Assistant > >> > Canadian Surgical Technologies & Advanced > Robotics > >> > Brain and Mind Institute > >> > Western University > >> > London, ON, N6A 5B7 > >> > Canada > >> > > >> > > >> > > >> > _______________________________________________ > >> > 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>> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> <mailto: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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > >> > > >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > >> <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>>> > >> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> > >> <http://www.partners.org/complianceline <http://www.partners.org/complianceline> > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > >> <mailto: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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>> > >> > >> -- > >> Douglas N. 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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> > <mailto: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> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > -- > Douglas N. 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Hi,
When i try running make_folding_atlas I get
xhemireg Trout2016 Wed Nov 2 13:11:23 EDT 2016 #@# xhemireg --s Trout2016 pbsubmit: Command not found. Launched 9 xhemireg processes #%# Waiting for 9 xhemireg processes Wed Nov 2 13:11:33 EDT 2016 #%# Waiting for 9 xhemireg processes Wed Nov 2 13:12:33 EDT 2016
I do not have access to a cluster. is there any way to bypass this?
Thank you,
Daiana
On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
I've written a script that will come out with version 6, but I've put it here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
I think it should work in 5.3, but I'm not sure. If not, you can download the dev version and make the atlas using that. Run it with --help to get info on how to run it.
On 10/28/2016 05:10 PM, Daya P wrote:
Hi Doug,
I needed to make a registration template and an cortical atlas because I am trying to measure cortical thickness, GM and surface area on cat brains.
What would be the necessary changes? Would it be possible (and appropriate) to use just mris_left_right_register instead?
Daiana
On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
A difference of 10 out of 500 or 1000 does not both me at all. Why do you need to create your own atlas? It is doable for the cross hemi stuff, it is just difficult. On 10/26/16 10:16 AM, Daya P wrote:Thank you for your help! I created a registration template and atlas from scratch could I input that in the interhemispheric registration analysis? The ROIs for the diffrerent regions per hemisphere are 50-100 vertices On Oct 24, 2016 5:03 PM, "Douglas N Greve" <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>wrote:
It would depend on how big the ROI is to begin with. Do you know that we have our own interhemispheric analysis that might be better for this? Check out http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> On 10/24/2016 12:33 PM, Daya P wrote: > Hi Bruce, > > I drew ROIs on an initial subject and then after registering all other > subjects to the initial one, used mri_label2label to map the ROIs from > the initial subject to subsequent ones. > I am interested in looking at asymmetry between left and right regions. > > I had two concerns, one that the ROIs have different # vertices on > different subjects, but as you mentioned the nonlinear process makes > sense, since each subject does not have the exact same brain size and > curvature. > > Another concern was that the ROIs on the left and right hemisphere in > a subject do not have the exact same number of vertices. Would a > difference of 10 vertices max bias results? > > Thank you for your help, > > Daiana R. Pur > Research Assistant > Canadian Surgical Technologies & Advanced Robotics > Brain and Mind Institute > Western University > London, ON, N6A 5B7 > Canada > > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: > > Hi Daiana > > yes, that is to be expected given the nonlinear nature of the > cross-subject registration. It shouldn't bias things, although > you'll need to give us more details if you want a more definitive > answer. > > cheers > Bruce > > > > On Mon, 24 Oct 2016, Daya P wrote: > > Hi All, > > My question is about using mri_label2label. When mapping the > labels from one > subject to another the number of vertices of each ROI is > different. Is that > something to be expected? > > How much of a difference does a number of vertices of 50 > compare to 40 have > on measures like thickness, grey matter and surface area? > > I would really appreciate some help > > Thank you, > > Daiana R. Pur > Research Assistant > Canadian Surgical Technologies & Advanced Robotics > Brain and Mind Institute > Western University > London, ON, N6A 5B7 > Canada > > > > _______________________________________________ > 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <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> -- 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 <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/ <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 <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>_______________________________________________ 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
oh, sorry, it does assume that you have pbsubmit, I had forgotten that. You can actually follow the instructions for building your own atlas at the bottom of the xhemi web page
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
This does the same thing as make_folding_atlas. It takes a long time if you don't have a computational cluster to submit it to, which is why I wrote make_folding_atlas
doug
On 11/02/2016 01:15 PM, Daya P wrote:
Hi,
When i try running make_folding_atlas I get
xhemireg Trout2016 Wed Nov 2 13:11:23 EDT 2016 #@# xhemireg --s Trout2016 pbsubmit: Command not found. Launched 9 xhemireg processes #%# Waiting for 9 xhemireg processes Wed Nov 2 13:11:33 EDT 2016 #%# Waiting for 9 xhemireg processes Wed Nov 2 13:12:33 EDT 2016
I do not have access to a cluster. is there any way to bypass this?
Thank you,
Daiana
On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I've written a script that will come out with version 6, but I've put it here https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas <https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas> I think it should work in 5.3, but I'm not sure. If not, you can download the dev version and make the atlas using that. Run it with --help to get info on how to run it. On 10/28/2016 05:10 PM, Daya P wrote: > Hi Doug, > > I needed to make a registration template and an cortical atlas because > I am trying to measure cortical thickness, GM and surface area on cat > brains. > > What would be the necessary changes? > Would it be possible (and appropriate) to use just > mris_left_right_register instead? > > Daiana > > On Fri, Oct 28, 2016 at 11:34 AM, 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: > > A difference of 10 out of 500 or 1000 does not both me at all. Why > do you need to create your own atlas? It is doable for the cross > hemi stuff, it is just difficult. > > > On 10/26/16 10:16 AM, Daya P wrote: >> >> Thank you for your help! >> >> I created a registration template and atlas from scratch could I >> input that in the interhemispheric registration analysis? >> >> The ROIs for the diffrerent regions per hemisphere are 50-100 >> vertices >> >> On Oct 24, 2016 5:03 PM, "Douglas N 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: >> >> It would depend on how big the ROI is to begin with. Do you >> know that we >> have our own interhemispheric analysis that might be better >> for this? >> Check out >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi <http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi>> >> >> >> On 10/24/2016 12:33 PM, Daya P wrote: >> > Hi Bruce, >> > >> > I drew ROIs on an initial subject and then after >> registering all other >> > subjects to the initial one, used mri_label2label to map >> the ROIs from >> > the initial subject to subsequent ones. >> > I am interested in looking at asymmetry between left and >> right regions. >> > >> > I had two concerns, one that the ROIs have different # >> vertices on >> > different subjects, but as you mentioned the nonlinear >> process makes >> > sense, since each subject does not have the exact same >> brain size and >> > curvature. >> > >> > Another concern was that the ROIs on the left and right >> hemisphere in >> > a subject do not have the exact same number of vertices. >> Would a >> > difference of 10 vertices max bias results? >> > >> > Thank you for your help, >> > >> > Daiana R. Pur >> > Research Assistant >> > Canadian Surgical Technologies & Advanced Robotics >> > Brain and Mind Institute >> > Western University >> > London, ON, N6A 5B7 >> > Canada >> > >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl >> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: >> > >> > Hi Daiana >> > >> > yes, that is to be expected given the nonlinear nature >> of the >> > cross-subject registration. It shouldn't bias things, >> although >> > you'll need to give us more details if you want a more >> definitive >> > answer. >> > >> > cheers >> > Bruce >> > >> > >> > >> > On Mon, 24 Oct 2016, Daya P wrote: >> > >> > Hi All, >> > >> > My question is about using mri_label2label. When >> mapping the >> > labels from one >> > subject to another the number of vertices of each >> ROI is >> > different. Is that >> > something to be expected? >> > >> > How much of a difference does a number of vertices >> of 50 >> > compare to 40 have >> > on measures like thickness, grey matter and surface >> area? >> > >> > I would really appreciate some help >> > >> > Thank you, >> > >> > Daiana R. Pur >> > Research Assistant >> > Canadian Surgical Technologies & Advanced Robotics >> > Brain and Mind Institute >> > Western University >> > London, ON, N6A 5B7 >> > Canada >> > >> > >> > >> > _______________________________________________ >> > 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>> >> <mailto: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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> >> > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <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> >> <http://www.partners.org/complianceline <http://www.partners.org/complianceline>> >> > <http://www.partners.org/complianceline <http://www.partners.org/complianceline> >> <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> >> <mailto: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> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel: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: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> >> <https://gate.nmr.mgh.harvard.edu/filedrop2 <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> >> <http://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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>> >> >> _______________________________________________ >> 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 <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <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> >> <mailto: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> >> <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> > <mailto: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> > <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> > <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> -- 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 <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/ <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 <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,
Thank you for your reply, when I run xhemireg I get an error for cannot find aseg. is there any way to avoid that? in the way there is a noaseg flag for other commmands. I built a cortical Atlas and dont have subcortical labels
Thank you ,
Daiana
Daiana Pur
On Wed, Nov 2, 2016 at 2:48 PM -0400, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
oh, sorry, it does assume that you have pbsubmit, I had forgotten that. You can actually follow the instructions for building your own atlas at the bottom of the xhemi web page
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
This does the same thing as make_folding_atlas. It takes a long time if you don't have a computational cluster to submit it to, which is why I wrote make_folding_atlas
doug
On 11/02/2016 01:15 PM, Daya P wrote:
Hi,
When i try running make_folding_atlas I get
xhemireg Trout2016 Wed Nov 2 13:11:23 EDT 2016 #@# xhemireg --s Trout2016 pbsubmit: Command not found. Launched 9 xhemireg processes #%# Waiting for 9 xhemireg processes Wed Nov 2 13:11:33 EDT 2016 #%# Waiting for 9 xhemireg processes Wed Nov 2 13:12:33 EDT 2016
I do not have access to a cluster. is there any way to bypass this?
Thank you,
Daiana
On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve
wrote:
I've written a script that will come out with version 6, but I've put it here https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas I think it should work in 5.3, but I'm not sure. If not, you can download the dev version and make the atlas using that. Run it with --help to get info on how to run it. On 10/28/2016 05:10 PM, Daya P wrote: > Hi Doug, > > I needed to make a registration template and an cortical atlas because > I am trying to measure cortical thickness, GM and surface area on cat > brains. > > What would be the necessary changes? > Would it be possible (and appropriate) to use just > mris_left_right_register instead? > > Daiana > > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve > >> wrote: > > A difference of 10 out of 500 or 1000 does not both me at all. Why > do you need to create your own atlas? It is doable for the cross > hemi stuff, it is just difficult. > > > On 10/26/16 10:16 AM, Daya P wrote: >> >> Thank you for your help! >> >> I created a registration template and atlas from scratch could I >> input that in the interhemispheric registration analysis? >> >> The ROIs for the diffrerent regions per hemisphere are 50-100 >> vertices >> >> On Oct 24, 2016 5:03 PM, "Douglas N Greve" >> >> wrote: >> >> It would depend on how big the ROI is to begin with. Do you >> know that we >> have our own interhemispheric analysis that might be better >> for this? >> Check out >> >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi >> > >> >> >> On 10/24/2016 12:33 PM, Daya P wrote: >> > Hi Bruce, >> > >> > I drew ROIs on an initial subject and then after >> registering all other >> > subjects to the initial one, used mri_label2label to map >> the ROIs from >> > the initial subject to subsequent ones. >> > I am interested in looking at asymmetry between left and >> right regions. >> > >> > I had two concerns, one that the ROIs have different # >> vertices on >> > different subjects, but as you mentioned the nonlinear >> process makes >> > sense, since each subject does not have the exact same >> brain size and >> > curvature. >> > >> > Another concern was that the ROIs on the left and right >> hemisphere in >> > a subject do not have the exact same number of vertices. >> Would a >> > difference of 10 vertices max bias results? >> > >> > Thank you for your help, >> > >> > Daiana R. Pur >> > Research Assistant >> > Canadian Surgical Technologies & Advanced Robotics >> > Brain and Mind Institute >> > Western University >> > London, ON, N6A 5B7 >> > Canada >> > >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl >> > >> > >> >> >>> wrote: >> > >> > Hi Daiana >> > >> > yes, that is to be expected given the nonlinear nature >> of the >> > cross-subject registration. It shouldn't bias things, >> although >> > you'll need to give us more details if you want a more >> definitive >> > answer. >> > >> > cheers >> > Bruce >> > >> > >> > >> > On Mon, 24 Oct 2016, Daya P wrote: >> > >> > Hi All, >> > >> > My question is about using mri_label2label. When >> mapping the >> > labels from one >> > subject to another the number of vertices of each >> ROI is >> > different. Is that >> > something to be expected? >> > >> > How much of a difference does a number of vertices >> of 50 >> > compare to 40 have >> > on measures like thickness, grey matter and surface >> area? >> > >> > I would really appreciate some help >> > >> > Thank you, >> > >> > Daiana R. Pur >> > Research Assistant >> > Canadian Surgical Technologies & Advanced Robotics >> > Brain and Mind Institute >> > Western University >> > London, ON, N6A 5B7 >> > Canada >> > >> > >> > >> > _______________________________________________ >> > 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 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 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 > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Try adding --zilles --reg
It is a hack, but it might just work
On 11/04/2016 07:34 AM, daianapur94@gmail.com wrote:
Hi,
Thank you for your reply, when I run xhemireg I get an error for cannot find aseg. is there any way to avoid that? in the way there is a noaseg flag for other commmands. I built a cortical Atlas and dont have subcortical labels
Thank you , Daiana Daiana Pur
On Wed, Nov 2, 2016 at 2:48 PM -0400, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
oh, sorry, it does assume that you have pbsubmit, I had forgotten that. You can actually follow the instructions for building your own atlas at the bottom of the xhemi web page http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi This does the same thing as make_folding_atlas. It takes a long time if you don't have a computational cluster to submit it to, which is why I wrote make_folding_atlas doug On 11/02/2016 01:15 PM, Daya P wrote: > Hi, > > When i try running make_folding_atlas I get > > xhemireg Trout2016 Wed Nov 2 13:11:23 EDT 2016 > #@# xhemireg --s Trout2016 > pbsubmit: Command not found. > Launched 9 xhemireg processes > #%# Waiting for 9 xhemireg processes Wed Nov 2 13:11:33 EDT 2016 > #%# Waiting for 9 xhemireg processes Wed Nov 2 13:12:33 EDT 2016 > > I do not have access to a cluster. is there any way to bypass this? > > Thank you, > > Daiana > > On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve >> wrote: > > I've written a script that will come out with version 6, but I've > put it > here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas > > > I think it should work in 5.3, but I'm not sure. If not, you can > download the dev version and make the atlas using that. Run it with > --help to get info on how to run it. > > > > On 10/28/2016 05:10 PM, Daya P wrote: > > Hi Doug, > > > > I needed to make a registration template and an cortical atlas > because > > I am trying to measure cortical thickness, GM and surface area > on cat > > brains. > > > > What would be the necessary changes? > > Would it be possible (and appropriate) to use just > > mris_left_right_register instead? > > > > Daiana > > > > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve > > > >> wrote: > > > > A difference of 10 out of 500 or 1000 does not both me at > all. Why > > do you need to create your own atlas? It is doable for the cross > > hemi stuff, it is just difficult. > > > > > > On 10/26/16 10:16 AM, Daya P wrote: > >> > >> Thank you for your help! > >> > >> I created a registration template and atlas from scratch > could I > >> input that in the interhemispheric registration analysis? > >> > >> The ROIs for the diffrerent regions per hemisphere are 50-100 > >> vertices > >> > >> On Oct 24, 2016 5:03 PM, "Douglas N Greve" > >> > >> wrote: > >> > >> It would depend on how big the ROI is to begin with. Do you > >> know that we > >> have our own interhemispheric analysis that might be better > >> for this? > >> Check out > >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > > >> > > >> > >> > >> On 10/24/2016 12:33 PM, Daya P wrote: > >> > Hi Bruce, > >> > > >> > I drew ROIs on an initial subject and then after > >> registering all other > >> > subjects to the initial one, used mri_label2label to map > >> the ROIs from > >> > the initial subject to subsequent ones. > >> > I am interested in looking at asymmetry between left and > >> right regions. > >> > > >> > I had two concerns, one that the ROIs have different # > >> vertices on > >> > different subjects, but as you mentioned the nonlinear > >> process makes > >> > sense, since each subject does not have the exact same > >> brain size and > >> > curvature. > >> > > >> > Another concern was that the ROIs on the left and right > >> hemisphere in > >> > a subject do not have the exact same number of vertices. > >> Would a > >> > difference of 10 vertices max bias results? > >> > > >> > Thank you for your help, > >> > > >> > Daiana R. Pur > >> > Research Assistant > >> > Canadian Surgical Technologies & Advanced Robotics > >> > Brain and Mind Institute > >> > Western University > >> > London, ON, N6A 5B7 > >> > Canada > >> > > >> > On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl > >> > > >> > > >> > >> >>> wrote: > >> > > >> > Hi Daiana > >> > > >> > yes, that is to be expected given the nonlinear > nature > >> of the > >> > cross-subject registration. It shouldn't bias things, > >> although > >> > you'll need to give us more details if you want a > more > >> definitive > >> > answer. > >> > > >> > cheers > >> > Bruce > >> > > >> > > >> > > >> > On Mon, 24 Oct 2016, Daya P wrote: > >> > > >> > Hi All, > >> > > >> > My question is about using mri_label2label. When > >> mapping the > >> > labels from one > >> > subject to another the number of vertices of each > >> ROI is > >> > different. Is that > >> > something to be expected? > >> > > >> > How much of a difference does a number of > vertices > >> of 50 > >> > compare to 40 have > >> > on measures like thickness, grey matter and > surface > >> area? > >> > > >> > I would really appreciate some help > >> > > >> > Thank you, > >> > > >> > Daiana R. Pur > >> > Research Assistant > >> > Canadian Surgical Technologies & Advanced > Robotics > >> > Brain and Mind Institute > >> > Western University > >> > London, ON, N6A 5B7 > >> > Canada > >> > > >> > > >> > > >> > _______________________________________________ > >> > 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 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 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 > > > > > 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I went to the shell script and changed the input for aparc+aseg and aseg. and managed to make it work.
My other question is that now that I have it running, after it is done I would like to run a vertex wise analysis.
Is there a tutorial/help or command that I should apply to do asymmetry analysis. I was looking at the group analysis and setting GLM for thickness and age. How could I do that with the results of xhemi for asymmetry in left and right hemisphere?
Thank you for you help!
On Nov 4, 2016, at 10:31 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Try adding --zilles --reg
It is a hack, but it might just work
On 11/04/2016 07:34 AM, daianapur94@gmail.com mailto:daianapur94@gmail.com wrote:
Hi,
Thank you for your reply, when I run xhemireg I get an error for cannot find aseg. is there any way to avoid that? in the way there is a noaseg flag for other commmands. I built a cortical Atlas and dont have subcortical labels
Thank you , Daiana Daiana Pur
On Wed, Nov 2, 2016 at 2:48 PM -0400, "Douglas N 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:
oh, sorry, it does assume that you have pbsubmit, I had forgotten that. You can actually follow the instructions for building your own atlas at the bottom of the xhemi web page
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
This does the same thing as make_folding_atlas. It takes a long time if you don't have a computational cluster to submit it to, which is why I wrote make_folding_atlas
doug
On 11/02/2016 01:15 PM, Daya P wrote:
Hi,
When i try running make_folding_atlas I get
xhemireg Trout2016 Wed Nov 2 13:11:23 EDT 2016 #@# xhemireg --s Trout2016 pbsubmit: Command not found. Launched 9 xhemireg processes #%# Waiting for 9 xhemireg processes Wed Nov 2 13:11:33 EDT 2016 #%# Waiting for 9 xhemireg processes Wed Nov 2 13:12:33 EDT 2016
I do not have access to a cluster. is there any way to bypass this?
Thank you,
Daiana
On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve
wrote: > > I've written a script that will come out with version
6, but I've > put it > here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
I think it should work in 5.3, but I'm not sure. If not, you
can > download the dev version and make the atlas using that. Run it with > --help to get info on how to run it. > > > > On 10/28/2016 05:10 PM, Daya P wrote: > > Hi Doug, > > > > I needed to make a registration template and an cortical atlas > because >
I am trying to measure cortical thickness, GM and surface area >
on cat > > brains. > > > > What would be the necessary changes? >
Would it be possible (and appropriate) to use just > >
mris_left_right_register instead? > > > > Daiana > > > > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve > > > >> wrote: > > > > A difference of 10 out of 500 or 1000 does not both me at > all. Why
do you need to create your own atlas? It is doable for the
cross > > hemi stuff, it is just difficult. > > > > > > On 10/26/16 10:16 AM, Daya P wrote: > >> > >> Thank you for your help! > >> > >> I created a registration template and atlas from scratch > could I > >> input that in the interhemispheric registration analysis? > >> > >> The ROIs for the diffrerent regions per hemisphere are 50-100 > >> vertices > >> > >> On Oct 24, 2016 5:03 PM, "Douglas N Greve" > >> > >> wrote: > >> > >> It would depend on how big the ROI is to begin with. Do you > >> know that we > >> have our own interhemispheric analysis that might be better > >> for this? > >> Check out > >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi > > >> > > >> > >>
On 10/24/2016 12:33 PM, Daya P wrote: > >> > Hi Bruce, > >> >
I drew ROIs on an initial subject and then after > >>
registering all other > >> > subjects to the initial one, used mri_label2label to map > >> the ROIs from > >> > the initial subject to subsequent ones. > >> > I am interested in looking at asymmetry between left and > >> right regions. > >> > > >> > I had two concerns, one that the ROIs have different # > >> vertices on
different subjects, but as you mentioned the nonlinear > >>
process makes > >> > sense, since each subject does not have the exact same > >> brain size and > >> > curvature. > >> > > >> > Another concern was that the ROIs on the left and right > >> hemisphere in > >> > a subject do not have the exact same number of vertices. > >> Would a > >> > difference of 10 vertices max bias results? > >> > > >> > Thank you for your help, > >> > > >> > Daiana R. Pur > >> > Research Assistant > >> > Canadian Surgical Technologies & Advanced Robotics > >> > Brain and Mind Institute >
Western University > >> > London, ON, N6A 5B7 > >> > Canada >
>>> On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl > >> > >>>>>>>>> wrote: > >> > > >> > Hi Daiana > >> > > >> >
yes, that is to be expected given the nonlinear > nature > >> of the > >> > cross-subject registration. It shouldn't bias things, >
although > >> > you'll need to give us more details if you want
a > more > >> definitive > >> > answer. > >> > > >> > cheers > >>
Bruce > >> > > >> > > >> > > >> > On Mon, 24 Oct 2016, Daya P
wrote: > >> > > >> > Hi All, > >> > > >> > My question is about using mri_label2label. When > >> mapping the > >> > labels from one > >> > subject to another the number of vertices of each > >> ROI is > >> > different. Is that > >> > something to be expected?
>>>> How much of a difference does a number of > vertices
of 50 > >> > compare to 40 have > >> > on measures like
thickness, grey matter and > surface > >> area? > >> > > >> > I would really appreciate some help > >> > > >> > Thank you, > >> >
Daiana R. Pur > >> > Research Assistant > >> > Canadian
Surgical Technologies & Advanced > Robotics > >> > Brain and Mind Institute > >> > Western University > >> > London, ON, N6A 5B7 >
Canada > >> > > >> > > >> > > >> >
_______________________________________________ > >> > 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 > >
>>>>>> -- > >> 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 > > >> > > >> 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 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
> 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
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 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
-- 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 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/ 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You should be able to apply the mris_preproc command on the xhemi page
https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
substituting your average subject for fsaverage_sym
On 11/04/2016 10:41 AM, Daya P wrote:
I went to the shell script and changed the input for aparc+aseg and aseg. and managed to make it work.
My other question is that now that I have it running, after it is done I would like to run a vertex wise analysis.
Is there a tutorial/help or command that I should apply to do asymmetry analysis. I was looking at the group analysis and setting GLM for thickness and age. How could I do that with the results of xhemi for asymmetry in left and right hemisphere?
Thank you for you help!
On Nov 4, 2016, at 10:31 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Try adding --zilles --reg
It is a hack, but it might just work
On 11/04/2016 07:34 AM,daianapur94@gmail.com mailto:daianapur94@gmail.comwrote:
Hi,
Thank you for your reply, when I run xhemireg I get an error for cannot find aseg. is there any way to avoid that? in the way there is a noaseg flag for other commmands. I built a cortical Atlas and dont have subcortical labels
Thank you , Daiana Daiana Pur
On Wed, Nov 2, 2016 at 2:48 PM -0400, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu> wrote:
oh, sorry, it does assume that you have pbsubmit, I had forgotten that. You can actually follow the instructions for building your own atlas at the bottom of the xhemi web page
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
This does the same thing as make_folding_atlas. It takes a long time if you don't have a computational cluster to submit it to, which is why I wrote make_folding_atlas
doug
On 11/02/2016 01:15 PM, Daya P wrote:
Hi,
When i try running make_folding_atlas I get
xhemireg Trout2016 Wed Nov 2 13:11:23 EDT 2016 #@# xhemireg --s Trout2016 pbsubmit: Command not found. Launched 9 xhemireg processes #%# Waiting for 9 xhemireg processes Wed Nov 2 13:11:33 EDT 2016 #%# Waiting for 9 xhemireg processes Wed Nov 2 13:12:33 EDT 2016
I do not have access to a cluster. is there any way to bypass this?
Thank you,
Daiana
On Tue, Nov 1, 2016 at 12:51 PM, Douglas N Greve
wrote: > > I've written a script that will come out with version
6, but I've > put it > here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas
I think it should work in 5.3, but I'm not sure. If not, you
can > download the dev version and make the atlas using that. Run it with > --help to get info on how to run it. > > > > On 10/28/2016 05:10 PM, Daya P wrote: > > Hi Doug, > > > > I needed to make a registration template and an cortical atlas > because >
I am trying to measure cortical thickness, GM and surface area >
on cat > > brains. > > > > What would be the necessary changes? >
Would it be possible (and appropriate) to use just > >
mris_left_right_register instead? > > > > Daiana > > > > On Fri, Oct 28, 2016 at 11:34 AM, Douglas Greve > > > >> wrote: > > > > A difference of 10 out of 500 or 1000 does not both me at > all. Why
do you need to create your own atlas? It is doable for the
cross > > hemi stuff, it is just difficult. > > > > > > On 10/26/16 10:16 AM, Daya P wrote: > >> > >> Thank you for your help! > >> > >> I created a registration template and atlas from scratch > could I > >> input that in the interhemispheric registration analysis? > >> > >> The ROIs for the diffrerent regions per hemisphere are 50-100 > >> vertices > >> > >> On Oct 24, 2016 5:03 PM, "Douglas N Greve" > >> > >> wrote: > >> > >> It would depend on how big the ROI is to begin with. Do you > >> know that we > >> have our own interhemispheric analysis that might be better > >> for this? > >> Check out > >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi%3E > >> > > >> > >>
On 10/24/2016 12:33 PM, Daya P wrote: > >> > Hi Bruce, > >> > > I drew ROIs on an initial subject and then after > >>
registering all other > >> > subjects to the initial one, used mri_label2label to map > >> the ROIs from > >> > the initial subject to subsequent ones. > >> > I am interested in looking at asymmetry between left and > >> right regions. > >> > > >> > I had two concerns, one that the ROIs have different # > >> vertices on
> different subjects, but as you mentioned the nonlinear > >>
process makes > >> > sense, since each subject does not have the exact same > >> brain size and > >> > curvature. > >> > > >> > Another concern was that the ROIs on the left and right > >> hemisphere in > >> > a subject do not have the exact same number of vertices. > >> Would a > >> > difference of 10 vertices max bias results? > >> > > >> > Thank you for your help, > >> > > >> > Daiana R. Pur > >> > Research Assistant > >> > Canadian Surgical Technologies & Advanced Robotics > >> > Brain and Mind Institute >
Western University > >> > London, ON, N6A 5B7 > >> > Canada > >>>> On Mon, Oct 24, 2016 at 12:09 PM, Bruce Fischl > >> > >>>>>>>>>> wrote: > >> > > >> > Hi Daiana > >> > > >> >
yes, that is to be expected given the nonlinear > nature > >> of the > >> > cross-subject registration. It shouldn't bias things, >
although > >> > you'll need to give us more details if you want
a > more > >> definitive > >> > answer. > >> > > >> > cheers > >>
Bruce > >> > > >> > > >> > > >> > On Mon, 24 Oct 2016, Daya P
wrote: > >> > > >> > Hi All, > >> > > >> > My question is about using mri_label2label. When > >> mapping the > >> > labels from one > >> > subject to another the number of vertices of each > >> ROI is > >> > different. Is that > >> > something to be expected?
>>>>> How much of a difference does a number of > vertices of 50 > >> > compare to 40 have > >> > on measures like
thickness, grey matter and > surface > >> area? > >> > > >> > I would really appreciate some help > >> > > >> > Thank you, > >> >
> Daiana R. Pur > >> > Research Assistant > >> > Canadian
Surgical Technologies & Advanced > Robotics > >> > Brain and Mind Institute > >> > Western University > >> > London, ON, N6A 5B7 >
Canada > >> > > >> > > >> > > >> >
_______________________________________________ > >> > Freesurfer mailing list > >> >Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu> > >> > > >> >
>>>>>>>>
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%3E > >> > > >> > > >> >> . 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%3E >
>>>>>>> -- > >> 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 > >
>>>>>>>>>>>>>
_______________________________________________ > >> 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. > > > > _______________________________________________ > > 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 > > >
_______________________________________________ > 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
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
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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Bruce Fischl -
daianapur94＠gmail.com -
Daya P
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Douglas Greve -
Douglas N Greve