Hi Michell, you appear to have two FreeSurfer analysis for this subject: /usr/local/freesurfer/subjects/ld12 /usr/local/freesurfer/subjects/retinotopy/sj12
Can you verify that these are *exactly* the same? doug Michelle Umali wrote: > Hi Doug and Freesurfers, > No matter what I try I am still getting the Dimension mismatch error > when running fieldsign-sess. I even ran recon-all -s sj12 -make all. > > I don't think it's a problem with the directories (below). The > subjectname file is correct, and when I run field-sign-sess it sees > the anatomical directory. > > What else do you recommend? > > Thanks. > Michelle > > > > On Mon, Oct 3, 2011 at 4:36 PM, Michelle Umali <mumal...@gmail.com > <mailto:mumal...@gmail.com>> wrote: > > Hi Doug, > I keep my retinotopy (sj) and anatomical (ld) data separate. I > named the retinotopy directory sj12 with the subjectname file > says ld12, which is the anatomical directory for the same subject. > > -Michelle > > > On Mon, Oct 3, 2011 at 4:31 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Can you check that the subjectname file is correct? In some > cases, it looks like it is using subject sj12, in others it > looks like it is using subject ld12. > doug > > Michelle Umali wrote: > > Hi Doug, > > I re-ran from preproc-sess using the -force flag, and I > still get the same dimension mismatch error. > > I'm attaching the terminal output starting from pre-proc-sess. > > What's the next step? > > Thanks. > Michelle > > On Mon, Oct 3, 2011 at 3:23 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: > > 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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto: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>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto: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>>> > <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 > <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> > <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 > <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>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto: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>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> <tel: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>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel: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> > > <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> > > <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> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto: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>> > <mailto: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>> > <tel: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>> > <tel: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> > > <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> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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
