Hi Doug, We have an old EPI data set where automatic (preproc-sess) or bbregister with any init type give a bad result. Hence, we are attempting to use a manual register.dat file instead. However, we must be doing something wrong, because changing preproc-sess to use our manual register.dat (done a couple of years ago) seems to have no effect. I suspect our preproc-sess options as not set up correctly. Our goal is to present the results on fsaverage surface.
Our preproc-sess command line is as follows: preproc-sess -s avml07 -fwhm 5 -surface fsaverage lhrh -per-session -sliceorder siemens -force -fsd bold -noreg -regfile bold/register.dat The whole analysis script is at /space/adapt/1/users/tapsya/project_AVISI_avml07/avml07/Analysis_avml07_fsaverage.csh FS version = 5.1 machine = adapt (analysis running on cluster) setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs/ individual subject = avml07 surface analysis lhrh, results to be presented on fsaverage surface Total of 3 runs per analysis (each with different number of TRs) Total of categories in mkanalysis-sess = 18 (9 main plus 9 rare target) FIR analysis Thank you for the advice in advance! Bests, Tommi --- Tommi Raij, MD, PhD MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. _______________________________________________ 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.
