Hello Freesurfers,
I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed.
Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects?
Thank you very much!
Sincerely, Ye
Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug
On 4/6/14 6:09 PM, ye tian wrote:
Hello Freesurfers,
I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed.
Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects?
Thank you very much!
Sincerely, Ye
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that "mris_preproc" gives "an average subject". How can this be an appropriate "data" for GLM, which for sure needs multiple data points?
Thank you!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug
On 4/6/14 6:09 PM, ye tian wrote:
Hello Freesurfers,
I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed.
Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects?
Thank you very much!
Sincerely, Ye
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.
It resamples them to a common space (the "average" subject) but does not average them together. The result is a "stack" which is a single file with multiple subject it in it ready for GLM analysis doug
On 4/6/14 6:18 PM, ye tian wrote:
Dear Doug,
Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that "mris_preproc" gives "an average subject". How can this be an appropriate "data" for GLM, which for sure needs multiple data points?
Thank you!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug On 4/6/14 6:09 PM, ye tian wrote:Hello Freesurfers, I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed. Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects? Thank you very much! Sincerely, Ye _______________________________________________ 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
Thank you very much!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:32 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
It resamples them to a common space (the "average" subject) but does not average them together. The result is a "stack" which is a single file with multiple subject it in it ready for GLM analysis doug
On 4/6/14 6:18 PM, ye tian wrote:
Dear Doug,
Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that "mris_preproc" gives "an average subject". How can this be an appropriate "data" for GLM, which for sure needs multiple data points?
Thank you!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug
On 4/6/14 6:09 PM, ye tian wrote:
Hello Freesurfers,
I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed.
Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects?
Thank you very much!
Sincerely, Ye
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.
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.
Hello Freesurfers,
Is there a way that I can take a look at the content of the output of " mris_preproc"?
Thank you very much!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:33 PM, ye tian tianye730@gmail.com wrote:
Dear Doug,
Thank you very much!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:32 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
It resamples them to a common space (the "average" subject) but does not average them together. The result is a "stack" which is a single file with multiple subject it in it ready for GLM analysis doug
On 4/6/14 6:18 PM, ye tian wrote:
Dear Doug,
Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that "mris_preproc" gives "an average subject". How can this be an appropriate "data" for GLM, which for sure needs multiple data points?
Thank you!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug
On 4/6/14 6:09 PM, ye tian wrote:
Hello Freesurfers,
I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed.
Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects?
Thank you very much!
Sincerely, Ye
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.
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.
It is just a script so you can view it with any text editor doug
On 6/18/14 7:15 PM, ye tian wrote:
Hello Freesurfers,
Is there a way that I can take a look at the content of the output of "mris_preproc"?
Thank you very much!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:33 PM, ye tian <tianye730@gmail.com mailto:tianye730@gmail.com> wrote:
Dear Doug, Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: It resamples them to a common space (the "average" subject) but does not average them together. The result is a "stack" which is a single file with multiple subject it in it ready for GLM analysis doug On 4/6/14 6:18 PM, ye tian wrote:Dear Doug, Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that "mris_preproc" gives "an average subject". How can this be an appropriate "data" for GLM, which for sure needs multiple data points? Thank you! Sincerely, Ye On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug On 4/6/14 6:09 PM, ye tian wrote:Hello Freesurfers, I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed. Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects? Thank you very much! Sincerely, Ye _______________________________________________ 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_______________________________________________ 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
These files typically end with .mgh. I tired opening them with text editors and them typically give a file of unreadable characters like:
@&駺9<窣,@!礱@ ^@$圚@萗@.?@6%@.溋@*>鳣!址@+?@!编@3岰@ 祺@€錊7]@>@<E褸%N(?錹?諕驚]Z@?蔮@0MU@'灔 @+緌@2Pq@ %?@7?@*y7@ @,?y@ Sincerely, Ye
On Wed, Jun 18, 2014 at 12:40 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
It is just a script so you can view it with any text editor doug
On 6/18/14 7:15 PM, ye tian wrote:
Hello Freesurfers,
Is there a way that I can take a look at the content of the output of " mris_preproc"?
Thank you very much!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:33 PM, ye tian tianye730@gmail.com wrote:
Dear Doug,
Thank you very much!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:32 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
It resamples them to a common space (the "average" subject) but does not average them together. The result is a "stack" which is a single file with multiple subject it in it ready for GLM analysis doug
On 4/6/14 6:18 PM, ye tian wrote:
Dear Doug,
Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that "mris_preproc" gives "an average subject". How can this be an appropriate "data" for GLM, which for sure needs multiple data points?
Thank you!
Sincerely, Ye
On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug
On 4/6/14 6:09 PM, ye tian wrote:
Hello Freesurfers,
I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed.
Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects?
Thank you very much!
Sincerely, Ye
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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 . 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 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.
oh, sorry, I thought you wanted to look at the script itself. The .mgh files are binary files with pixel data. You can view them with tksurfer/freeview. You can load them with MRIread.m in matlab On 6/18/14 8:41 PM, ye tian wrote:
Dear Doug,
These files typically end with .mgh. I tired opening them with text editors and them typically give a file of unreadable characters like:
@&?9<?,@!?@ ^@$?@?@.?@6%@.?@*>?!?@+?@!?@3?@ ?@EUR?7]@>?@<E?%N(?????]Z@??@0MU@'? @+?@2Pq@%?@7?@*y7@ ?@,?y@ Sincerely, Ye
On Wed, Jun 18, 2014 at 12:40 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
It is just a script so you can view it with any text editor doug On 6/18/14 7:15 PM, ye tian wrote:Hello Freesurfers, Is there a way that I can take a look at the content of the output of "mris_preproc"? Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:33 PM, ye tian <tianye730@gmail.com <mailto:tianye730@gmail.com>> wrote: Dear Doug, Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:32 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: It resamples them to a common space (the "average" subject) but does not average them together. The result is a "stack" which is a single file with multiple subject it in it ready for GLM analysis doug On 4/6/14 6:18 PM, ye tian wrote:Dear Doug, Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that "mris_preproc" gives "an average subject". How can this be an appropriate "data" for GLM, which for sure needs multiple data points? Thank you! Sincerely, Ye On Sun, Apr 6, 2014 at 5:12 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug On 4/6/14 6:09 PM, ye tian wrote:Hello Freesurfers, I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed. Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects? Thank you very much! Sincerely, Ye _______________________________________________ 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_______________________________________________ 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_______________________________________________ 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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freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
ye tian