As I said before, I would average the T1weighed images that vbm puts in mni152 space, then run recon-all on that
On 3/14/19 6:06 AM, Laboratorio de Neurociencia Funcional wrote: > > External Email - Use Caution > > Dear Doug, > > please let me know if it is possible to run the recon-all to the > fsaverage subject of my sample to obtain specific labels (from the > aparc+aseg.mgz and the aparc.a2009s+aseg.mgz files) derived from my > analysis sample. > > Many thanks in advance. > > Best, > Jose > > El mar., 12 mar. 2019 a las 18:17, Laboratorio de Neurociencia > Funcional (<neuroaging...@gmail.com <mailto:neuroaging...@gmail.com>>) > escribió: > > I just want to use some labels contained in the aparc+aseg.mgz and > the aparc.a2009s+aseg.mgz files to build an anatomical template > that can be used in VBM analysis. To my understanding, these > labels should be obtained from the entire sample since they will > be used as the anatomical template for VBM analysis. For that > reason, I decided to run the recon-all to my fsaverage subject and > take the labels of interest. Is it the right way to proceed? > > Thank you in advance. > > Best, > Jose > > El mar., 12 mar. 2019 a las 17:58, Greve, Douglas N.,Ph.D. > (<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>) escribió: > > I'm still not sure what you are trying to do. If you are > running vbm, > you can usually get the T1 sampled in the MNI space for all > subjects. > You can average them together and run the average through > recon-all > > On 3/12/19 11:44 AM, Laboratorio de Neurociencia Funcional wrote: > > > > External Email - Use Caution > > > > Hi Bruce, > > > > what I really need is to obtain several labels that are only > included > > in the aparc+aseg, not for each subject but for the entire > sample. My > > goal is to use these labels (ROIs) in VBM analysis after > they are > > trasformed to volume and further registered to MNI. To this > aim, I > > though to obtain first the fsaverage subject from my sample, > run the > > recon-all in that fsaverage, and finally obtain the labels of > > interest. Is there another way to proceed with this? > > > > Thank you in advance. > > > > Best, > > Jose > > > > El mar., 12 mar. 2019 a las 14:55, Bruce Fischl > > (<fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>>) > > escribió: > > > > Hi Jose > > > > can you clarify what you mean by "...to get all the > labels that are > > obtained in each individual subject." You almost > certainly don't > > need to > > recon fsaverage to do this, but I'm not sure exactly > what you mean > > > > cheers > > Bruce > > > > > > On Tue, 12 > > Mar 2019, Laboratorio de Neurociencia Funcional wrote: > > > > > > > > External Email - Use Caution > > > > > > Dear Freesurfers, > > > > > > I would like to apply recon-all to the fsaverage > subject of my > > sample to get all the labels that are > > > obtained in each individual subject. However, it is > not possible > > because my average subject doesn't > > > contain the file /orig/001.mgz required to run the > recon-all. > > Could you help me to handle this > > > issue? > > > > > > Many thanks in advance. > > > > > > Best regards, > > > Jose > > > > > >_______________________________________________ > > 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 > > > > > > _______________________________________________ > > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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
