[Freesurfer] (no subject)
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Re: [Freesurfer] .mgh file not load into surfstats
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>: > 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>: > >> 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>: >>> 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 >>> 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 sen
Re: [Freesurfer] .mgh file not load into surfstats
Great! Many thanks!! 2015-09-28 16:56 GMT-04:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > 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 ag
Re: [Freesurfer] .mgh file not load into surfstats
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>: > 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>: >> 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>: >> 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>: >> 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.fsave
Re: [Freesurfer] .mgh file not load into surfstats
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>: > 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>: >> 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 >> 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 > > > 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 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.
Re: [Freesurfer] .mgh file not load into surfstats
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>: > 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 > 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 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] .mgh file not load into surfstats
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 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.
