Hi
Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec?
That would be great if I can get an answer in more detail since I have seen the post in FAQ, just need more information in detail regarding calculating the power !
We don't have a way to do a power analysis directly from QDEC. I have some matlab code that does it for univariate analysis.
In the QDEC output folder, you will see a glm folder. In that there will be folders for each contrast. In the contrast folder, you will see an F.mgh file which will be the F-values. You can convert this to a t = sign(gamma.mgh)*sqrt(F)
doug
On 10/28/2013 07:27 AM, amirhossein manzouri wrote:
Hi Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? That would be great if I can get an answer in more detail since I have seen the post in FAQ, just need more information in detail regarding calculating the power ! -- Best regards, Amirhossein Manzouri
Thanks Doug, Would you please provide me the MATLAB code and instruction! BR
On Tue, Oct 29, 2013 at 3:25 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
We don't have a way to do a power analysis directly from QDEC. I have some matlab code that does it for univariate analysis.
In the QDEC output folder, you will see a glm folder. In that there will be folders for each contrast. In the contrast folder, you will see an F.mgh file which will be the F-values. You can convert this to a t = sign(gamma.mgh)*sqrt(F)
doug
On 10/28/2013 07:27 AM, amirhossein manzouri wrote:
Hi Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? That would be great if I can get an answer in more detail since I have seen the post in FAQ, just need more information in detail regarding calculating the power ! -- 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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The matlab code is here:
$FREESURFER_HOME/fsfast/toolbox/fast_glmpower.m
There's not much documentation on it. Have you done power analyses before?
doug
On 10/29/2013 10:29 AM, amirhossein manzouri wrote:
Thanks Doug, Would you please provide me the MATLAB code and instruction! BR
On Tue, Oct 29, 2013 at 3:25 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
We don't have a way to do a power analysis directly from QDEC. I have some matlab code that does it for univariate analysis. In the QDEC output folder, you will see a glm folder. In that there will be folders for each contrast. In the contrast folder, you will see an F.mgh file which will be the F-values. You can convert this to a t = sign(gamma.mgh)*sqrt(F) doug On 10/28/2013 07:27 AM, amirhossein manzouri wrote: Hi Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? That would be great if I can get an answer in more detail since I have seen the post in FAQ, just need more information in detail regarding calculating the power ! -- 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/ 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
One comment on power calculations. You cannot do the power calculations after you have completed the study. Any reviewer/referee asking you to compute the power should be politely informed that post-hoc power analyses are not valid and are biased (because you would be computing the power of the observed effect).
What you want to do is to compute the power of the experiment before you conduct the experiment. You want to be able to say that to compare an effect of X, we have have Y% power to detect the effect with N subjects.
G*Power is an excellent program to compute power - although it doesn't do it on the entire image.
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 29, 2013 at 10:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
We don't have a way to do a power analysis directly from QDEC. I have some matlab code that does it for univariate analysis.
In the QDEC output folder, you will see a glm folder. In that there will be folders for each contrast. In the contrast folder, you will see an F.mgh file which will be the F-values. You can convert this to a t = sign(gamma.mgh)*sqrt(F)
doug
On 10/28/2013 07:27 AM, amirhossein manzouri wrote:
Hi Would you please let me know if it is possible to calculate the power
for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec?
That would be great if I can get an answer in more detail since I have seen the post in FAQ, just need more information in detail regarding calculating the power ! -- 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/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Good point Donald. Where can one get G*Power? doug
On 10/29/2013 10:38 AM, MCLAREN, Donald wrote:
One comment on power calculations. You cannot do the power calculations after you have completed the study. Any reviewer/referee asking you to compute the power should be politely informed that post-hoc power analyses are not valid and are biased (because you would be computing the power of the observed effect).
What you want to do is to compute the power of the experiment before you conduct the experiment. You want to be able to say that to compare an effect of X, we have have Y% power to detect the effect with N subjects.
G*Power is an excellent program to compute power - although it doesn't do it on the entire image.
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 29, 2013 at 10:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
We don't have a way to do a power analysis directly from QDEC. I have some matlab code that does it for univariate analysis. In the QDEC output folder, you will see a glm folder. In that there will be folders for each contrast. In the contrast folder, you will see an F.mgh file which will be the F-values. You can convert this to a t = sign(gamma.mgh)*sqrt(F) doug On 10/28/2013 07:27 AM, amirhossein manzouri wrote: > Hi > Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? > That would be great if I can get an answer in more detail since I have > seen the post in FAQ, just need more information in detail regarding > calculating the power ! > -- > 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/ _______________________________________________ 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.
For anyone who wants G*Power, here is a link to the download page. It is free for all users.
http://www.psycho.uni-duesseldorf.de/abteilungen/aap/gpower3/
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 29, 2013 at 10:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Good point Donald. Where can one get G*Power? doug
On 10/29/2013 10:38 AM, MCLAREN, Donald wrote:
One comment on power calculations. You cannot do the power calculations after you have completed the study. Any reviewer/referee asking you to compute the power should be politely informed that post-hoc power analyses are not valid and are biased (because you would be computing the power of the observed effect).
What you want to do is to compute the power of the experiment before you conduct the experiment. You want to be able to say that to compare an effect of X, we have have Y% power to detect the effect with N subjects.
G*Power is an excellent program to compute power - although it doesn't do it on the entire image.
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/~**mclarenhttp://www.martinos.org/~mclaren< http://www.martinos.org/%**7Emclaren 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 29, 2013 at 10:25 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
We don't have a way to do a power analysis directly from QDEC. I have some matlab code that does it for univariate analysis. In the QDEC output folder, you will see a glm folder. In that there will be folders for each contrast. In the contrast folder, you will see an F.mgh file which will be the F-values. You can convert this to a t = sign(gamma.mgh)*sqrt(F) doug On 10/28/2013 07:27 AM, amirhossein manzouri wrote: > Hi > Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? > That would be great if I can get an answer in more detail since I have > seen the post in FAQ, just need more information in detail regarding > calculating the power ! > -- > 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/> ______________________________**_________________ 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.-- 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/
Thanks a lot Doug and Donald for useful information!
On Tue, Oct 29, 2013 at 3:51 PM, MCLAREN, Donald mclaren.donald@gmail.comwrote:
For anyone who wants G*Power, here is a link to the download page. It is free for all users.
http://www.psycho.uni-duesseldorf.de/abteilungen/aap/gpower3/
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 29, 2013 at 10:40 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Good point Donald. Where can one get G*Power? doug
On 10/29/2013 10:38 AM, MCLAREN, Donald wrote:
One comment on power calculations. You cannot do the power calculations after you have completed the study. Any reviewer/referee asking you to compute the power should be politely informed that post-hoc power analyses are not valid and are biased (because you would be computing the power of the observed effect).
What you want to do is to compute the power of the experiment before you conduct the experiment. You want to be able to say that to compare an effect of X, we have have Y% power to detect the effect with N subjects.
G*Power is an excellent program to compute power - although it doesn't do it on the entire image.
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/~**mclarenhttp://www.martinos.org/~mclaren< http://www.martinos.org/%**7Emclarenhttp://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 29, 2013 at 10:25 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edugreve@nmr.mgh.harvard.edu>> wrote:
We don't have a way to do a power analysis directly from QDEC. I have some matlab code that does it for univariate analysis. In the QDEC output folder, you will see a glm folder. In that there will be folders for each contrast. In the contrast folder, you will see an F.mgh file which will be the F-values. You can convert this to a t = sign(gamma.mgh)*sqrt(F) doug On 10/28/2013 07:27 AM, amirhossein manzouri wrote: > Hi > Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? > That would be great if I can get an answer in more detail since I have > seen the post in FAQ, just need more information in detailregarding > calculating the power ! > -- > 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/> ______________________________**_________________ 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.-- 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/
Here is a paper discussing post-experiment power analyses and why they are wrong: http://amstat.tandfonline.com/doi/abs/10.1198/000313001300339897#.Um_aDtexGk...
On 10/29/2013 10:51 AM, MCLAREN, Donald wrote:
For anyone who wants G*Power, here is a link to the download page. It is free for all users.
http://www.psycho.uni-duesseldorf.de/abteilungen/aap/gpower3/
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 29, 2013 at 10:40 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Good point Donald. Where can one get G*Power? doug On 10/29/2013 10:38 AM, MCLAREN, Donald wrote: One comment on power calculations. You cannot do the power calculations after you have completed the study. Any reviewer/referee asking you to compute the power should be politely informed that post-hoc power analyses are not valid and are biased (because you would be computing the power of the observed effect). What you want to do is to compute the power of the experiment before you conduct the experiment. You want to be able to say that to compare an effect of X, we have have Y% power to detect the effect with N subjects. G*Power is an excellent program to compute power - although it doesn't do it on the entire image. 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> <http://www.martinos.org/%7Emclaren> Office: (773) 406-2464 <tel:%28773%29%20406-2464> ===================== 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 29, 2013 at 10:25 AM, 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: We don't have a way to do a power analysis directly from QDEC. I have some matlab code that does it for univariate analysis. In the QDEC output folder, you will see a glm folder. In that there will be folders for each contrast. In the contrast folder, you will see an F.mgh file which will be the F-values. You can convert this to a t = sign(gamma.mgh)*sqrt(F) doug On 10/28/2013 07:27 AM, amirhossein manzouri wrote: > Hi > Would you please let me know if it is possible to calculate the power for a group comparison in cortical thickness? Also, a referee is requesting F-values and T map , are they generated by q-dec? > That would be great if I can get an answer in more detail since I have > seen the post in FAQ, just need more information in detail regarding > calculating the power ! > -- > Best regards, > Amirhossein Manzouri > > -- 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. -- 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/
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amirhossein manzouri -
Chris Watson -
Douglas N Greve -
MCLAREN, Donald