Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html). I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template.
Thanks! Caspar
I've put that script here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc
On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote:
Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html). I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template.
Thanks! Caspar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug, that's great, thank you very much.
From the previous posts I assume that this does not solve the issue with
the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar
2013/8/19 Douglas N Greve greve@nmr.mgh.harvard.edu
I've put that script here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc
On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote:
Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before (
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html).
I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template.
Thanks! Caspar
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.
I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run
tkregister2 --fstal --s subject
It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effect on statistics, but it will affect the appearance of the pial and white surfaces (if you display your results on those instead of on the inflated). If you are not going to display on the white or the pial, then you can just leave it as the identity
doug
On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, that's great, thank you very much. From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar
2013/8/19 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
I've put that script here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: > Hi Freesurfer experts, > I am trying to make an average surface from several monkey surfaces, > and I ran into a problem with make_average_subject. Specifically, I do > not have an aparc file nor a talairach.xfm. It seems that these > problems have come up on the list before > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html). > I tried to download make_average_surface.no-aparc, however, the link > seems to be broken. Also, I couldn't find a solution to the missing > talairach.xfm on the list. > It would be great if you could provide me with a working link to > make_average_surface.no-aparc; any suggestions regarding making an > average surface without talairach.xfm would be appreciated. > I already made a new template and aligned all individual surfaces to > this template. > > Thanks! > Caspar > > > > _______________________________________________ > 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.
Hi Doug, I ran make_average_surface.no-aparc and identity matrices on my data, and I seems to have completed the averaging without an error. However, when I try to view the result with tksurfer, I get an error because there is no average T1 for the average subject. How would you recommend I go about this? Do you have a make_average_volume.no-aparc as well, shall I make an average T1 manually, or can I skip the average T1? Thanks! Caspar
2013/8/19 Douglas N Greve greve@nmr.mgh.harvard.edu
I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run
tkregister2 --fstal --s subject
It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effect on statistics, but it will affect the appearance of the pial and white surfaces (if you display your results on those instead of on the inflated). If you are not going to display on the white or the pial, then you can just leave it as the identity
doug
On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, that's great, thank you very much. From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar
2013/8/19 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto: greve@nmr.mgh.harvard.**edu greve@nmr.mgh.harvard.edu>>
I've put that script here ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/make_average_surface.no-**aparcftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc
On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: > Hi Freesurfer experts, > I am trying to make an average surface from several monkey surfaces, > and I ran into a problem with make_average_subject. Specifically, I do > not have an aparc file nor a talairach.xfm. It seems that these > problems have come up on the list before > (http://www.mail-archive.com/**freesurfer@nmr.mgh.harvard.**edu/msg15595.htmlhttp://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html ). > I tried to download make_average_surface.no-aparc, however, the link > seems to be broken. Also, I couldn't find a solution to the missing > talairach.xfm on the list. > It would be great if you could provide me with a working link to > make_average_surface.no-aparc; any suggestions regarding making an > average surface without talairach.xfm would be appreciated. > I already made a new template and aligned all individual surfaces to > this template. > > Thanks! > Caspar > > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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/
You can just copy in the T1.mgz from fsaverage (won't matter that it is human), or you can try running make_average_volume to make a NHP volume. Not sure that will work, but make sure to use --no-aseg
doug
On 8/19/13 8:43 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, I ran make_average_surface.no-aparc and identity matrices on my data, and I seems to have completed the averaging without an error. However, when I try to view the result with tksurfer, I get an error because there is no average T1 for the average subject. How would you recommend I go about this? Do you have a make_average_volume.no-aparc as well, shall I make an average T1 manually, or can I skip the average T1? Thanks! Caspar
2013/8/19 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run tkregister2 --fstal --s subject It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effect on statistics, but it will affect the appearance of the pial and white surfaces (if you display your results on those instead of on the inflated). If you are not going to display on the white or the pial, then you can just leave it as the identity doug On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, that's great, thank you very much. From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar 2013/8/19 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>>> I've put that script here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: > Hi Freesurfer experts, > I am trying to make an average surface from several monkey surfaces, > and I ran into a problem with make_average_subject. Specifically, I do > not have an aparc file nor a talairach.xfm. It seems that these > problems have come up on the list before > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html). > I tried to download make_average_surface.no-aparc, however, the link > seems to be broken. Also, I couldn't find a solution to the missing > talairach.xfm on the list. > It would be great if you could provide me with a working link to > make_average_surface.no-aparc; any suggestions regarding making an > average surface without talairach.xfm would be appreciated. > I already made a new template and aligned all individual surfaces to > this template. > > Thanks! > Caspar > > > > _______________________________________________ > 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 -- 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/
Hi Doug, just a quick follow-up on my previous questions regarding custom average surfaces. I guess I am a bit confused regarding the relationship of custom templates and custom average surfaces. I made a custom template and a custom average surface. However, I don't understand how they are related to each other. Furthermore, I am wondering which is used when I use rawfunc2surface-sess. Thanks, Caspar
2013/8/19 Douglas Greve greve@nmr.mgh.harvard.edu
You can just copy in the T1.mgz from fsaverage (won't matter that it is human), or you can try running make_average_volume to make a NHP volume. Not sure that will work, but make sure to use --no-aseg
doug
On 8/19/13 8:43 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, I ran make_average_surface.no-aparc and identity matrices on my data, and I seems to have completed the averaging without an error. However, when I try to view the result with tksurfer, I get an error because there is no average T1 for the average subject. How would you recommend I go about this? Do you have a make_average_volume.no-aparc as well, shall I make an average T1 manually, or can I skip the average T1? Thanks! Caspar
2013/8/19 Douglas N Greve greve@nmr.mgh.harvard.edu
I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run
tkregister2 --fstal --s subject
It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effect on statistics, but it will affect the appearance of the pial and white surfaces (if you display your results on those instead of on the inflated). If you are not going to display on the white or the pial, then you can just leave it as the identity
doug
On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote:
Hi Doug, that's great, thank you very much. From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar
2013/8/19 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: greve@nmr.mgh.harvard.edu>
I've put that script hereftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc
On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: > Hi Freesurfer experts, > I am trying to make an average surface from several monkeysurfaces, > and I ran into a problem with make_average_subject. Specifically, I do > not have an aparc file nor a talairach.xfm. It seems that these > problems have come up on the list before > ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html ). > I tried to download make_average_surface.no-aparc, however, the link > seems to be broken. Also, I couldn't find a solution to the missing > talairach.xfm on the list. > It would be great if you could provide me with a working link to > make_average_surface.no-aparc; any suggestions regarding making an > average surface without talairach.xfm would be appreciated. > I already made a new template and aligned all individual surfaces to > this template. > > Thanks! > Caspar > > > > _______________________________________________ > 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
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Caspar M. Schwiedrzik -
Douglas Greve -
Douglas N Greve