That template is part of the distribution, in $FREESURFER_HOME/subjects/fsaverage
On 09/28/2015 03:07 PM, Myriam Oliver wrote: > Hi Bruce! > > I convert from the individual space to the talairach space, but the > target (--trgsubject) was the first subject from my data, that was > pick randomly. > mri_surf2surf --s ' subjectid ' --hemi lh --sval-tal-xyz white --tval > talairach.white --tval-xyz --trgsubject ' subjectid01 > > I think it will be better to convert it adding as a target the "fsaverage" > > So, I am wondering how can I get that template > > Thanks again for your time and patience > > 2015-09-28 14:51 GMT-04:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>: > > Hi Myriam > > sorry, I don't understand. What do you ean by "compare it with the > cortical surface of fsaverage"? What are you trying to compare? > > cheers > Bruce > > On Mon, 28 Sep 2015, Myriam Oliver wrote: > > Hi again! > > When I transform from the individual space to the average, I > was doing it the command line. > To ensure the results are ok, I want to compare it with the > cortical surface of the Freesurfer's > average subject (fsaverage) > Where can I find that template? > > Thanks in advance for your help and time! > Myriam > > 2015-09-26 20:29 GMT-04:00 Myriam Oliver > <myriam.oliv...@gmail.com <mailto:myriam.oliv...@gmail.com>>: > Hi! > many thanks both for your responses, they were very very useful! > So, at the end I was not transforming properly (from the > individual space to the average). > After doing it, it works! > Many thanks! > > 2015-09-25 8:59 GMT-04:00 Bruce Fischl > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>: > Hi Myriam > > sorry, I don't know SurfStat at all so I don't really > understand the error. Can you > run mris_info on your transformed surfaces and confirm > that they have the same > number of vertices? If you are transforming .mgh files > note that they are *NOT* > surfaces, but scalar fields over the surface. They can > be transformed with > mri_surf2surf, but you wouldn't use --tval-xyz and such. > > cheers > Bruce > > On Fri, 25 Sep 2015, Myriam Oliver wrote: > > Hi Bruce! > Thank you for your response. Sorry about the > incomplete information, > > I need the average surface of each participant, so > for me it will be > great > to use the output already generated for > freesurfer. However, it is not > read > by surfstats. So, one solution was to change to > .mgh format to .obj > > The solution two can be use the lh.white which > surfstats reads and > change > the matrix dimensions so I can compare all > subjects. This is the command > I > use for each subject to change the matrix dimensions: > > mri_surf2surf --s ' subjectid ' --hemi lh > --sval-tal-xyz white --tval > talairach.white --tval-xyz --trgsubject ' subjectid > > %Average surface > > left_files = SurfStatListDir([cd filesep > 'lh.white.transform'], []); > right_files = SurfStatListDir([cd filesep > 'rh.white.transform'], []); > f = [left_files, right_files]; > avsurf = SurfStatAvSurf(f); > > The error is: > Error using + Matrix dimensions must agree. > Error in SurfStatAvSurf (line 36) > surf.coord=fun(surf.coord,double(s.coord)); > > > Thank you! > > 2015-09-24 15:50 GMT-04:00 Bruce Fischl > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>: > when you say "it does not work either', what > do you mean? Please > remember > to send us the entire screen output of > commands you are asking > about > On Thu, > 24 Sep 2015, Myriam Oliver wrote: > > > Dear Freesurfers, > > > > I wanted to ask you if you know how can I > convert a .mgh file > to a .obj > > file. > > > > I want to run surfstats (specifically > SurfStatReadSurf ) but > it does not > > read .mgh files (i.e, the surface file; > lh.w-g.pct.mgh.fsaverage.mgh). > > Although, it reads the lh.white, but I > need the average, as > otherwise I have > > an error of matrix dimension between subjects. > > > > I try using the lh.white and changing the > matrix dimensions > through: > > mri_surf2surf --s ' subjectid ' --hemi lh > --sval-tal-xyz white > --tval > > talairach.white --tval-xyz --trgsubject ' > subjectid > > > > But it does not work either. > > > > Any help about how can I use the .mgh file > in surfstats? > > > > Thanks! > > > > > _______________________________________________ > 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. > > > > > -- > Myriam > > > _______________________________________________ > 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. > > > > > -- > Myriam > > > > > -- > Myriam > > > _______________________________________________ > 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. > > > > > -- > /* > Myriam > */ > > > _______________________________________________ > 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 gr...@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
