You can an asynchrony between your fmri data and the anatomical: Anatomical: num vertices: 146530 fMRI: 158944 vertices
re-run the fMRI starting from preproc-sess. You will need to make sure that preproc-sess actually re-runs at least the sample-to-surface. By default, it just looks to see if things are up-to-date (but does not check the anatomical). So, you can run it with -force. This will cause it to re-run everything. Or you can delete the surface files in the bold directories and re-run without -force. doug Michelle Umali wrote: > Hi Doug, > I've attached the mri_info output on the eccen and polar images as > well as the mris_info on the lh.sphere surface > > Thanks. > Michelle > > On Mon, Oct 3, 2011 at 2:38 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Can you send me the result of running mri_info on > eccen/real.nii > eccen/imag.nii > polar/real.nii > polar/imag.nii > in the > /usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh > directory? > > And the result of > mris_info > /usr/local/freesurfer/subjects/retinotopy/sj12/surf/lh.sphere > > doug > > > > > > Michelle Umali wrote: > > Hi Doug, > I've attached the output from running fieldsign-sess. > > Thanks for all your help. > Michelle > > On Mon, Oct 3, 2011 at 12:59 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > Michelle, before you do that, can you run the offending program > with -debug and send me the (copious) terminal output? Your > anat > should not have to be re-run. > > doug > > Michelle Umali wrote: > > Hi Bruce, > Will this undo my wm and pial edits? > > Thanks. > Michelle > > On Sat, Oct 1, 2011 at 3:37 PM, 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>> > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>>> wrote: > > try running > > > recon-all -s subject -make all > > and leave the -dontrun off. It should bring > everything up > to date > > Bruce > > > > On Sat, 1 Oct 2011, Michelle Umali wrote: > > Dear Freesurfers, > I'm still getting a MRISripZeros() and > MRIScopyMRI Surf/src > mismatch error > when running fieldsign-sess. You suggested that > this > problem > was due to the > surfaces being out of synch. When I ran > recon-all -s > subject > -make all > -dontrun, I saw that several steps had not run. > The data > looked alright and > the number of vertices matched when I ran > -vno-check. > > The mismatch error is still occurring, and I > don't know > how to > proceed. > > Please suggest steps that I should take. > > Thanks. > Michelle > > > > > > 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 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 > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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: > 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> > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
