Hi all, I am now working with the 5.3 version and performing interhemispheric registration (building my own atlas)
after running for all subjects: xhemireg --s subj001.... surfreg --s subj001 --t fsaverage_sym --lh surfreg --s subj001 --t fsaverage_sym --xhemi --lh I have tried first iteration, but the following error occurs: processing subject subj001 (1 of 194) reading spherical surface /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface how can I get the rh.fsaverage_sym.sphere.reg file? thank you! Angela > Hi Matt > > certainly something is wrong, but it's hard to tell why from the single > slice. You have big topological defects that are being fixed incorrectly. > Can you upload the subject and we will take a look? > cheers > Bruce > On Mon, 28 Jul 2014, > Walton, Matt wrote: > >> Hello Freesurfer team, >> I've used freesurfer to segment (recon-all) approximately 30 different >> subjects from a study. I've noticed that a large number of these >> subjects >> have a misclassification of the white and pial boundaries in the >> occipital >> lobe (such that grey matter is being classified as white matter). I >> believe >> this problem is originating from my scanner and original data. I'm >> acquiring >> a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 >> channel >> phased array head coil. For many subjects, this acquistion gives >> intensity >> inhomogeneity in the occipital lobe. I've begun using a GE based >> correction >> technique (PURE) on the images, and it appears to improve the intensity >> in >> the occipital lobe, but Freesurfer is still frequently misclassifying. >> >> I'm wondering what would be the best way to edit the data. I've often >> tried >> to edit the wm.vol, but this doesn't seem to fix anything. For the most >> part, the wm.vol is correct to begin with, but the wm cutting line isn't >> segmenting with the wm.vol. I've also tried to add control points but >> this >> doesn't seem to improve anything either. >> >> I've attached an image which I hope will further explain my problems. >> >> Thanks for any help >> >>_______________________________________________ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
