Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) 4) Is there any way to look at the results through the brain per slice and also the whole brain?
On 07/10/2013 01:26 AM, amirhossein manzouri wrote:
Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls.
- Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical
thickness difference between left and right hemisphere of each subject?
Yes.
- If yes, shouldn't I see the similar mapping by overlaying this to
lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh)
I don't know what you mean. Can you elaborate/
- How do you interpret the result after analyzing within one group?
( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh)
It is the difference between left and right hemisphere at each vertex.
- Is there any way to look at the results through the brain per slice
and also the whole brain?
Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug
-- Best regards, Amirhossein Manzouri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug, When I overlay the results on L & R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR
On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
On 07/10/2013 01:26 AM, amirhossein manzouri wrote:
Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40
controls.
- Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical
thickness difference between left and right hemisphere of each subject?
Yes.
- If yes, shouldn't I see the similar mapping by overlaying this to
lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh)
I don't know what you mean. Can you elaborate/
- How do you interpret the result after analyzing within one group?
( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh)
It is the difference between left and right hemisphere at each vertex.
- Is there any way to look at the results through the brain per slice
and also the whole brain?
Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug
-- Best regards, Amirhossein Manzouri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
I don't know what you mean by overlaying the results on L & R. What is your command line?
On 7/11/13 3:34 AM, amirhossein manzouri wrote:
Thanks Doug, When I overlay the results on L & R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR
On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
On 07/10/2013 01:26 AM, amirhossein manzouri wrote: > Dear Doug and FS experts, > I am trying to use Xhemi tool to study asymmetry in the brain. I have > done the exact procedure you mentioned in WiKi for a group of 40 controls. > 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical > thickness difference between left and right hemisphere of each subject? Yes. > 2) If yes, shouldn't I see the similar mapping by overlaying this to > lh and rh? > (tksurfer fsaverage_sym rh inflated -aparc -overlay > lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ > 3) How do you interpret the result after analyzing within one group? > ( tksurfer fsaverage_sym lh inflated -aparc -overlay > glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. > 4) Is there any way to look at the results through the brain per slice > and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug > > -- > Best regards, > Amirhossein Manzouri > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Best regards, Amirhossein Manzouri
As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR
On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
I don't know what you mean by overlaying the results on L & R. What is your command line?
On 7/11/13 3:34 AM, amirhossein manzouri wrote:
Thanks Doug, When I overlay the results on L & R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR
On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
On 07/10/2013 01:26 AM, amirhossein manzouri wrote:
Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40
controls.
- Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical
thickness difference between left and right hemisphere of each subject?
Yes.
- If yes, shouldn't I see the similar mapping by overlaying this to
lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh)
I don't know what you mean. Can you elaborate/
- How do you interpret the result after analyzing within one group?
( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh)
It is the difference between left and right hemisphere at each vertex.
- Is there any way to look at the results through the brain per slice
and also the whole brain?
Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug
-- Best regards, Amirhossein Manzouri
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Best regards, Amirhossein Manzouri
The first command loads the left hemisphere overlay onto the right hemisphere. Why do you want to do this? doug
On 07/11/2013 11:13 AM, amirhossein manzouri wrote:
As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR
On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I don't know what you mean by overlaying the results on L & R. What is your command line? On 7/11/13 3:34 AM, amirhossein manzouri wrote:Thanks Doug, When I overlay the results on L & R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: On 07/10/2013 01:26 AM, amirhossein manzouri wrote: > Dear Doug and FS experts, > I am trying to use Xhemi tool to study asymmetry in the brain. I have > done the exact procedure you mentioned in WiKi for a group of 40 controls. > 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical > thickness difference between left and right hemisphere of each subject? Yes. > 2) If yes, shouldn't I see the similar mapping by overlaying this to > lh and rh? > (tksurfer fsaverage_sym rh inflated -aparc -overlay > lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ > 3) How do you interpret the result after analyzing within one group? > ( tksurfer fsaverage_sym lh inflated -aparc -overlay > glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. > 4) Is there any way to look at the results through the brain per slice > and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug > > -- > Best regards, > Amirhossein Manzouri > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri-- Best regards, Amirhossein Manzouri
Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? I need to see the difference map of left and right (lh-rh) overlaid on both hemispheres!
On Thu, Jul 11, 2013 at 6:01 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
The first command loads the left hemisphere overlay onto the right hemisphere. Why do you want to do this? doug
On 07/11/2013 11:13 AM, amirhossein manzouri wrote:
As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR
On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve <greve@nmr.mgh.harvard.edu<mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>> wrote:
I don't know what you mean by overlaying the results on L & R. What is your command line? On 7/11/13 3:34 AM, amirhossein manzouri wrote:Thanks Doug, When I overlay the results on L & R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>>wrote:
On 07/10/2013 01:26 AM, amirhossein manzouri wrote: > Dear Doug and FS experts, > I am trying to use Xhemi tool to study asymmetry in the brain. I have > done the exact procedure you mentioned in WiKi for a group of 40 controls. > 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical > thickness difference between left and right hemisphere of each subject? Yes. > 2) If yes, shouldn't I see the similar mapping by overlaying this to > lh and rh? > (tksurfer fsaverage_sym rh inflated -aparc -overlay > lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ > 3) How do you interpret the result after analyzing within one group? > ( tksurfer fsaverage_sym lh inflated -aparc -overlay > glm.lh.lh-rh.thickness.sm05/**osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. > 4) Is there any way to look at the results through the brain per slice > and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug > > -- > Best regards, > Amirhossein Manzouri > > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: 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/
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri-- Best regards, Amirhossein Manzouri
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/
It is the difference but it is on the tesselation of the left hemisphere. If you want it on the right hemisphere, then you need to perform the analysis on the right hemisphere. doug
On 07/12/2013 02:37 AM, amirhossein manzouri wrote:
Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? I need to see the difference map of left and right (lh-rh) overlaid on both hemispheres!
On Thu, Jul 11, 2013 at 6:01 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The first command loads the left hemisphere overlay onto the right hemisphere. Why do you want to do this? doug On 07/11/2013 11:13 AM, amirhossein manzouri wrote: As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: I don't know what you mean by overlaying the results on L & R. What is your command line? On 7/11/13 3:34 AM, amirhossein manzouri wrote: Thanks Doug, When I overlay the results on L & R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 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: On 07/10/2013 01:26 AM, amirhossein manzouri wrote: > Dear Doug and FS experts, > I am trying to use Xhemi tool to study asymmetry in the brain. I have > done the exact procedure you mentioned in WiKi for a group of 40 controls. > 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical > thickness difference between left and right hemisphere of each subject? Yes. > 2) If yes, shouldn't I see the similar mapping by overlaying this to > lh and rh? > (tksurfer fsaverage_sym rh inflated -aparc -overlay > lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ > 3) How do you interpret the result after analyzing within one group? > ( tksurfer fsaverage_sym lh inflated -aparc -overlay > glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. > 4) Is there any way to look at the results through the brain per slice > and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug > > -- > Best regards, > Amirhossein Manzouri > > > > > _______________________________________________ > 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 -- 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> 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> <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> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/-- Best regards, Amirhossein Manzouri
Thanks a lot!
On Fri, Jul 12, 2013 at 6:58 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
It is the difference but it is on the tesselation of the left hemisphere. If you want it on the right hemisphere, then you need to perform the analysis on the right hemisphere. doug
On 07/12/2013 02:37 AM, amirhossein manzouri wrote:
Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? I need to see the difference map of left and right (lh-rh) overlaid on both hemispheres!
On Thu, Jul 11, 2013 at 6:01 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
The first command loads the left hemisphere overlay onto the right hemisphere. Why do you want to do this? doug On 07/11/2013 11:13 AM, amirhossein manzouri wrote: As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu>>>>wrote:
I don't know what you mean by overlaying the results on L & R. What is your command line? On 7/11/13 3:34 AM, amirhossein manzouri wrote: Thanks Doug, When I overlay the results on L & R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>>>>wrote:
On 07/10/2013 01:26 AM, amirhossein manzouri wrote: > Dear Doug and FS experts, > I am trying to use Xhemi tool to study asymmetry in the brain. I have > done the exact procedure you mentioned in WiKi for a group of 40 controls. > 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical > thickness difference between left and right hemisphere of each subject? Yes. > 2) If yes, shouldn't I see the similar mapping by overlaying this to > lh and rh? > (tksurfer fsaverage_sym rh inflated -aparc -overlay > lh.lh-rh.thickness.sm00.mgh) I don't know what you mean. Can you elaborate/ > 3) How do you interpret the result after analyzing within one group? > ( tksurfer fsaverage_sym lh inflated -aparc -overlay > glm.lh.lh-rh.thickness.sm05/**osgm/sig.mgh) It is the difference between left and right hemisphere at each vertex. > 4) Is there any way to look at the results through the brain per slice > and also the whole brain? Do you mean mapping the difference into the volume and then viewing it as a volume? If so, You can try mri_surf2vol doug > > -- > Best regards, > Amirhossein Manzouri > > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: 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/>-- Best regards, Amirhossein Manzouri
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/
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