Hi! Well, as far as I know: - both are MNI standards ---- Colin27 is the MNI Colin27 single subject standard ---- fsaverage is MNI305
My problem with fsaverage was that I couldn't use the transformations made with the registration matrix after spmregister or bbregister, but I understand that it depends on the application. This is the reason I used the alternative way through Colin27 (since both are the same brain, one in 2mm and the other in 1mm, the registration matrix was almost 1).
Saying that, I understand that if you want the AAL .labels in fsaverage, you always could use mri_label2label in order to transform every label to fsaverage.
I don't know what is the best method, maybe some expert in the list will be able to confirm this step, but it is definitely what I would do. If you are thinking using qdec or some other tool with fsaverage, I understand that you could always create your own average and transform the data there or create the data with mri_surf2surf for Colin27 (this is going to be our approach).
hope this helps! Gari
On Tue, Oct 23, 2012 at 7:15 PM, MCLAREN, Donald mclaren.donald@gmail.comwrote:
How does the Colin 27 space differ from MNI space in terms of freesurfer? Ideally, I'd want them to be useable with the standard FS Average surface that is in MNI space.
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.
On Tue, Oct 23, 2012 at 7:37 AM, Garikoitz Lerma-Usabiaga garikoitz@gmail.com wrote:
Hi Donald and everybody, I created AAL .mgh and .label-s in FS Colin27 space, if anybody is interested please drop me a line.
best regards! Gari
On Thu, Jul 12, 2012 at 11:12 PM, MCLAREN, Donald <
mclaren.donald@gmail.com>
wrote:
Has anyone created an AAL label file for Freesurfer? I've done some ROI analysis using AAL regions and want to display regional values on the freesurfer surface.
Best Regards, Donald McLaren
D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain
PROTECTED
HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If
the
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The information in this e-mail is intended only for the person to whom
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If you can get the AAL labels onto the surface, then the surface-based registration in mri_label2label would be best. doug
On 10/24/2012 07:01 AM, Garikoitz Lerma-Usabiaga wrote:
Hi! Well, as far as I know:
- both are MNI standards
---- Colin27 is the MNI Colin27 single subject standard ---- fsaverage is MNI305
My problem with fsaverage was that I couldn't use the transformations made with the registration matrix after spmregister or bbregister, but I understand that it depends on the application. This is the reason I used the alternative way through Colin27 (since both are the same brain, one in 2mm and the other in 1mm, the registration matrix was almost 1).
Saying that, I understand that if you want the AAL .labels in fsaverage, you always could use mri_label2label in order to transform every label to fsaverage.
I don't know what is the best method, maybe some expert in the list will be able to confirm this step, but it is definitely what I would do. If you are thinking using qdec or some other tool with fsaverage, I understand that you could always create your own average and transform the data there or create the data with mri_surf2surf for Colin27 (this is going to be our approach).
hope this helps! Gari
On Tue, Oct 23, 2012 at 7:15 PM, MCLAREN, Donald <mclaren.donald@gmail.com mailto:mclaren.donald@gmail.com> wrote:
How does the Colin 27 space differ from MNI space in terms of freesurfer? Ideally, I'd want them to be useable with the standard FS Average surface that is in MNI space. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren <http://www.martinos.org/%7Emclaren> Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Oct 23, 2012 at 7:37 AM, Garikoitz Lerma-Usabiaga <garikoitz@gmail.com <mailto:garikoitz@gmail.com>> wrote: > Hi Donald and everybody, > I created AAL .mgh and .label-s in FS Colin27 space, if anybody is > interested please drop me a line. > > best regards! > Gari > > On Thu, Jul 12, 2012 at 11:12 PM, MCLAREN, Donald <mclaren.donald@gmail.com <mailto:mclaren.donald@gmail.com>> > wrote: >> >> Has anyone created an AAL label file for Freesurfer? I've done some >> ROI analysis using AAL regions and want to display regional values on >> the freesurfer surface. >> >> Best Regards, Donald McLaren >> ================= >> D.G. McLaren, Ph.D. >> Research Fellow, Department of Neurology, Massachusetts General Hospital >> and >> Harvard Medical School >> Postdoctoral Research Fellow, GRECC, Bedford VA >> Website: http://www.martinos.org/~mclaren <http://www.martinos.org/%7Emclaren> >> Office: (773) 406-2464 >> ===================== >> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >> intended only for the use of the individual or entity named above. If the >> reader of the e-mail is not the intended recipient or the employee or >> agent >> responsible for delivering it to the intended recipient, you are hereby >> notified that you are in possession of confidential and privileged >> information. Any unauthorized use, disclosure, copying or the taking of >> any >> action in reliance on the contents of this information is strictly >> prohibited and may be unlawful. If you have received this e-mail >> unintentionally, please immediately notify the sender via telephone at >> (773) >> 406-2464 or email. >> _______________________________________________ >> 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. >> >
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-
Douglas N Greve -
Garikoitz Lerma-Usabiaga