Dear Freesurfer-list,
I have 2 questions: one regarding lesioned brains and another regarding kids’ brains.
1) All of our patients have large lesions on the left side. After the recon-all step, I used tkmedit brainmask.mgz and found that for some patients, the lesion location had been flipped from left to right (see attached). Any suggestions on how to solve this issue, prior to running a group level analysis?
2) We have preprocessed some images of typically-developing children (9-11yo). After recon-all, I checked the registration using tkregister2 --mgz –s --fstal --surf orig and found that the green line didn’t cover the surfaces well in most cases (see attached) . I’ve read in previous postings that Freesurfer should be fine with kids’ brains, so perhaps we don't need to modify them manually? Is there any other way to check for registration? Any other suggestions?
Many thanks in advance for your help!
Regards, Catherine
Hi Catherine
when you say "left" do you mean the left side of the image or the left side of the brain? In tkmedit the left side of the image will always represent the right side of the brain (as indicated by the little green "R" and arrow).
As for the goodness of the surface fit to talairach, that just is a function of the blurriness of the talairach coordinate system.
cheers Bruce
On Thu, 11 Aug 2011, Catherine Wan wrote:
Dear Freesurfer-list,
I have 2 questions: one regarding lesioned brains and another regarding kids? brains.
- All of our patients have large lesions on the left side. After the recon-all step, I used tkmedit brainmask.mgz and found that for some patients, the lesion location
had been flipped from left to right (see attached). Any suggestions on how to solve this issue, prior to running a group level analysis?
- We have preprocessed some images of typically-developing children (9-11yo). After recon-all, I checked the registration using tkregister2 --mgz ?s--fstal --surf orig and
found that the green line didn?t cover the surfaces well in most cases (see attached) . I?ve read in previous postings that Freesurfer should be fine with kids? brains, so perhaps we don't need to modify them manually? Is there any other way to check for registration? Any other suggestions?
Many thanks in advance for your help!
Regards, Catherine
Hi Bruce,
Thanks for your prompt response. I meant all lesions should be on the left side of the brain. So as you can see from the revised image (attached), the lesion of patient 1 has been flipped to the right side of the brain when viewed in tkmedit. Any suggestions?
Just to clarify. Are you saying that we can disregard the tkregister2 step for these healthy kids' brains, and run the group level analysis after recon-all is done?
Many thanks! Catherine
On Thu, Aug 11, 2011 at 3:25 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Catherine
when you say "left" do you mean the left side of the image or the left side of the brain? In tkmedit the left side of the image will always represent the right side of the brain (as indicated by the little green "R" and arrow).
As for the goodness of the surface fit to talairach, that just is a function of the blurriness of the talairach coordinate system.
cheers Bruce
On Thu, 11 Aug 2011, Catherine Wan wrote:
Dear Freesurfer-list,
I have 2 questions: one regarding lesioned brains and another regarding kids? brains.
- All of our patients have large lesions on the left side. After the
recon-all step, I used tkmedit brainmask.mgz and found that for some patients, the lesion location had been flipped from left to right (see attached). Any suggestions on how to solve this issue, prior to running a group level analysis?
- We have preprocessed some images of typically-developing children
(9-11yo). After recon-all, I checked the registration using tkregister2 --mgz ?s--fstal --surf orig and found that the green line didn?t cover the surfaces well in most cases (see attached) . I?ve read in previous postings that Freesurfer should be fine with kids? brains, so perhaps we don't need to modify them manually? Is there any other way to check for registration? Any other suggestions?
Many thanks in advance for your help!
Regards, Catherine
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/**compliancelinehttp://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.
what format are you using? Is it analyze?
And yes, Doug can confirm but I think that's as good as you are going to get for registering a subject's surfaces to a talairach average volume with a linear xform
On Thu, 11 Aug 2011, Catherine Wan wrote:
Hi Bruce,
Thanks for your prompt response. I meant all lesions should be on the left side of the brain. So as you can see from the revised image (attached), the lesion of patient 1 has been flipped to the right side of the brain when viewed in tkmedit. Any suggestions?
Just to clarify. Are you saying that we can disregard the tkregister2 step for these healthy kids' brains, and run the group level analysis after recon-all is done?
Many thanks! Catherine
On Thu, Aug 11, 2011 at 3:25 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Catherine
when you say "left" do you mean the left side of the image or the left side of the brain? In tkmedit the left side of the image will always represent the right side of the brain (as indicated by the little green "R" and arrow). As for the goodness of the surface fit to talairach, that just is a function of the blurriness of the talairach coordinate system. cheers BruceOn Thu, 11 Aug 2011, Catherine Wan wrote:
Dear Freesurfer-list, I have 2 questions: one regarding lesioned brains and another regarding kids? brains. 1) All of our patients have large lesions on the left side. After the recon-all step, I used tkmedit brainmask.mgz and found that for some patients, the lesion location had been flipped from left to right (see attached). Any suggestions on how to solve this issue, prior to running a group level analysis? 2) We have preprocessed some images of typically-developing children (9-11yo). After recon-all, I checked the registration using tkregister2 --mgz ?s--fstal --surf orig and found that the green line didn?t cover the surfaces well in most cases (see attached) . I?ve read in previous postings that Freesurfer should be fine with kids? brains, so perhaps we don't need to modify them manually? Is there any other way to check for registration? Any other suggestions? Many thanks in advance for your help! Regards, CatherineThe 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.
p.s. note that the image you show of the surface over the tal volume has a caption saying "surface registration", but in fact what you are showing is the talairach (volume) registration applied to the surface, *not* the surface registration. The easiest way to check the surface registration is to look at the accuracy of the ?h.aparc.annot. If it looks good then the surface registration worked.
On Thu, 11 Aug 2011, Catherine Wan wrote:
Dear Freesurfer-list,
I have 2 questions: one regarding lesioned brains and another regarding kids? brains.
- All of our patients have large lesions on the left side. After the recon-all step, I used tkmedit brainmask.mgz and found that for some patients, the lesion location
had been flipped from left to right (see attached). Any suggestions on how to solve this issue, prior to running a group level analysis?
- We have preprocessed some images of typically-developing children (9-11yo). After recon-all, I checked the registration using tkregister2 --mgz ?s--fstal --surf orig and
found that the green line didn?t cover the surfaces well in most cases (see attached) . I?ve read in previous postings that Freesurfer should be fine with kids? brains, so perhaps we don't need to modify them manually? Is there any other way to check for registration? Any other suggestions?
Many thanks in advance for your help!
Regards, Catherine
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Catherine Wan