Dear Freesurfers,
I would like to do some customized model fitting for cortical thickness. Is there a way to export freesurfer data into R or simply as a text?
Thank you very much!
Sincerely, Ye
sure, you can load them into matlab with read_surf.m and do whatever you want, or convert to ascii with for example:
mris_convert lh.orig lh.orig.asc
cheers Bruce On Thu, 27 Feb 2014, ye tian wrote:
Dear Freesurfers, I would like to do some customized model fitting for cortical thickness. Is there a way to export freesurfer data into R or simply as a text?
Thank you very much!
Sincerely, Ye
Can you be more specific about what you mean by "freesurfer data"? Each subject has 300MB of "data" doug
On 02/27/2014 10:48 PM, ye tian wrote:
Dear Freesurfers,
I would like to do some customized model fitting for cortical thickness. Is there a way to export freesurfer data into R or simply as a text?
Thank you very much!
Sincerely, Ye
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce and Doug,
Thank you very much!
Would you please tell me more about what "freesurfer data" actually is? Is it composed of pixel positions and intensities? If that's the case, how do you calculate cortical thickness?
Thank you very much!
Sincerely, Ye
On Fri, Feb 28, 2014 at 10:21 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Can you be more specific about what you mean by "freesurfer data"? Each subject has 300MB of "data" doug
On 02/27/2014 10:48 PM, ye tian wrote:
Dear Freesurfers,
I would like to do some customized model fitting for cortical thickness. Is there a way to export freesurfer data into R or simply as a text?
Thank you very much!
Sincerely, Ye
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.
Hi Ye
it is both that, and volumes of label indices (e.g. 17=Left Hippocampus) and surface models (triangles, edges, points) and scalar and vector fields over them.
cheers Bruce
On Mon, 3 Mar 2014, ye tian wrote:
Dear Bruce and Doug, Thank you very much!
Would you please tell me more about what "freesurfer data" actually is? Is it composed of pixel positions and intensities? If that's the case, how do you calculate cortical thickness?
Thank you very much!
Sincerely, Ye
On Fri, Feb 28, 2014 at 10:21 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you be more specific about what you mean by "freesurfer data"? Each subject has 300MB of "data" doug On 02/27/2014 10:48 PM, ye tian wrote: > Dear Freesurfers, > > I would like to do some customized model fitting for cortical > thickness. Is there a way to export freesurfer data into R or simply > as a text? > > Thank you very much! > > Sincerely, > Ye > >
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.
Dear Bruce and Doug,
Would you please shine some light on what the freesurfer files mean?
For example, rh.orig, once mris_converted, starts with
115750 231496 21.097221 -65.951393 -18.834326 0 20.621031 -66.165680 -18.995041 0 .....
I thought that this file gives all unidentified regions, since 0=unknown, but it doesn't make sense.
Furthermore, 1) What do the first two numbers mean? 2) Not all files can be fed into mris_convert. Do you recommend using read_surf.m instead?
Thank you very much!
Sincerely, Ye
On Tue, Mar 4, 2014 at 7:30 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Ye
it is both that, and volumes of label indices (e.g. 17=Left Hippocampus) and surface models (triangles, edges, points) and scalar and vector fields over them.
cheers Bruce
On Mon, 3 Mar 2014, ye tian wrote:
Dear Bruce and Doug,
Thank you very much!
Would you please tell me more about what "freesurfer data" actually is? Is it composed of pixel positions and intensities? If that's the case, how do you calculate cortical thickness?
Thank you very much!
Sincerely, Ye
On Fri, Feb 28, 2014 at 10:21 AM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Can you be more specific about what you mean by "freesurfer data"? Each subject has 300MB of "data" doug On 02/27/2014 10:48 PM, ye tian wrote: > Dear Freesurfers, > > I would like to do some customized model fitting for cortical > thickness. Is there a way to export freesurfer data into R or simply > as a text? > > Thank you very much! > > Sincerely, > Ye > >
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.
On 04/05/2014 09:49 PM, ye tian wrote:
Dear Bruce and Doug,
Would you please shine some light on what the freesurfer files mean?
For example, rh.orig, once mris_converted, starts with
115750 231496 21.097221 -65.951393 -18.834326 0 20.621031 -66.165680 -18.995041 0 .....
I thought that this file gives all unidentified regions, since 0=unknown, but it doesn't make sense.
Furthermore,
- What do the first two numbers mean?
I think the first is the number of vertices and the 2nd the number of faces
- Not all files can be fed into mris_convert. Do you recommend using
read_surf.m instead?
Thank you very much!
Sincerely, Ye
On Tue, Mar 4, 2014 at 7:30 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Ye it is both that, and volumes of label indices (e.g. 17=Left Hippocampus) and surface models (triangles, edges, points) and scalar and vector fields over them. cheers Bruce On Mon, 3 Mar 2014, ye tian wrote: Dear Bruce and Doug, Thank you very much! Would you please tell me more about what "freesurfer data" actually is? Is it composed of pixel positions and intensities? If that's the case, how do you calculate cortical thickness? Thank you very much! Sincerely, Ye On Fri, Feb 28, 2014 at 10:21 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Can you be more specific about what you mean by "freesurfer data"? Each subject has 300MB of "data" doug On 02/27/2014 10:48 PM, ye tian wrote: > Dear Freesurfers, > > I would like to do some customized model fitting for cortical > thickness. Is there a way to export freesurfer data into R or simply > as a text? > > 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 -- 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.
Dear Doug,
Thank you!
Sincerely, Ye
On Tue, Apr 8, 2014 at 4:47 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
On 04/05/2014 09:49 PM, ye tian wrote:
Dear Bruce and Doug,
Would you please shine some light on what the freesurfer files mean?
For example, rh.orig, once mris_converted, starts with
115750 231496 21.097221 -65.951393 -18.834326 0 20.621031 -66.165680 -18.995041 0 .....
I thought that this file gives all unidentified regions, since 0=unknown, but it doesn't make sense.
Furthermore,
- What do the first two numbers mean?
I think the first is the number of vertices and the 2nd the number of faces
- Not all files can be fed into mris_convert. Do you recommend using
read_surf.m instead?
Thank you very much!
Sincerely, Ye
On Tue, Mar 4, 2014 at 7:30 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto: fischl@nmr.mgh.harvard.edu> wrote:
Hi Ye it is both that, and volumes of label indices (e.g. 17=Left Hippocampus) and surface models (triangles, edges, points) and scalar and vector fields over them. cheers Bruce On Mon, 3 Mar 2014, ye tian wrote: Dear Bruce and Doug, Thank you very much! Would you please tell me more about what "freesurfer data" actually is? Is it composed of pixel positions and intensities? If that's the case, how do you calculate cortical thickness? Thank you very much! Sincerely, Ye On Fri, Feb 28, 2014 at 10:21 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: Can you be more specific about what you mean by "freesurfer data"? Each subject has 300MB of "data" doug On 02/27/2014 10:48 PM, ye tian wrote: > Dear Freesurfers, > > I would like to do some customized model fitting for cortical > thickness. Is there a way to export freesurfer data into R or simply > as a text? > > 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 -- 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.-- 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
ye tian