Hi Maryam, You should check your spm defaults to see whether it uses radiology or neurology convention. Most likely your spm has flipped your image, and the spmregister-sess is trying to match the left hemisphere of your functionals to the right hemisphere of your anatomical.
-Yuhong On Thu, Feb 3, 2011 at 9:59 PM, Maryam Vaziri Pashkam <mvazir...@gmail.com>wrote: > Hi, > > > I am new to freesurfer and I am analyzing fmri data on a Mac OSX 10.5.8 > computer using freesurfer 4.5. I have SPM 8 and FSL also installed. > > > I have two versions of matlab (matlab R2009b & R2008a) on my computer. I > think spm runs through the R2009b on my computer. I have added the SPM path > to the startup.m of both matlabs by adding the following line (they both > point to the same startup.m ): > > path(path,'/Applications/spm8'); > > > I run preprocessing on the data using the following command: > > preproc-sess -nosmooth -sf retino-sess -df retino.dir > > > then I run automatic registration with the following command: > > spmregister-sess -sf retino-sess -df retino.dir > > > It runs smoothly and there seems to be no errors. But when I try to check > the registration with this command: > > > tkregister-sess -sf retino-sess -df retino.dir -inorm > > > what I see is not a good registration. Isn't spm register supposed to do a > good job in automatic registration? The one that I get still needs a lot of > manual adjustment. Am I doing something wrong? I have attached the log files > for spmregister and tkregister and a screen shot of the image that I get > after running tkregister. I would appreciate any help in this matter. > > > > Thanks, > > Maryam > > > > _______________________________________________ > 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. > > -- ---------------------------------------------------------- Yuhong Vanessa Jiang, PhD, Associate Professor & McKnight Presidential Fellow Department of Psychology, Univ of Minnesota jiang...@umn.edu, 612-625-7003 https://sites.google.com/site/jiang166/ ----------------------------------------------------------
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