Hi Tommi, convert the w file to an mgz with mri_surf2surf. Specify the source format with --sfmt w doug
r...@nmr.mgh.harvard.edu wrote: > Hi Doug and Matti, > > I am using mri_surfcluster to threshold and extract ROIs from MEG/EEG > source analysis data. The same code used to work fine in Jan 2009, but now > I am running into unexpected errors. I wonder if something happened along > the way of FreeSurfer and/or MNE stream upgrades and now mne_analyze .w > files and mri_surfcluster no longer talk to each other. > > I first run the usual MEG/EEG analysis using the MNE stream and then save > the resulting dSPM map on the surface of the subject as a .w file (using > the mne_analyze GUI). For sanity check, I download the overlay in tksurfer > and observe that it looks fine (which makes me think that the problem > originates at the mri_surfcluster side rather than at mne_analyze; > however, see below for evidence suggesting the opposite). > > on machine adapt > nmr-std-env (=FreeSurfer 5.1) > mne_setup > cd /cluster/scratch/monday/raij/MEEG > setenv SUBJECTS_DIR /cluster/scratch/monday/raij/MRIs/ > setenv SUBJECT Wyss_000 > > mri_surfcluster \ > --subject Wyss_000 \ > --hemi lh \ > --in AVL_GA_List1-00150.0-lh.w \ > --frame 0 \ > --thmin 2 \ > --thsign abs \ > --minarea 100 \ > --olab test01 \ > > thsign = abs, id = 0 > version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $ > hemi = lh > srcid = AVL_GA_List1-00150.0-lh.w > srcsubjid = Wyss_000 > srcsurf = white > srcframe = 0 > thsign = abs > thmin = 2 > thmax = -1 > fdr = -1 > minarea = 100 > xfmfile = talairach.xfm > nth = -1 > subjectsdir = /cluster/scratch/monday/raij/MRIs/ > FixMNI = 1 > ------------- XFM matrix (RAS2RAS) --------------- > /cluster/scratch/monday/raij/MRIs//Wyss_000/mri/transforms/talairach.xfm > 0.973 -0.031 -0.031 0.033; > 0.001 0.989 0.327 -34.515; > 0.008 -0.285 1.073 -30.192; > 0.000 0.000 0.000 1.000; > ---------------------------------------------------- > Reading source surface > /cluster/scratch/monday/raij/MRIs//Wyss_000/surf/lh.white > Done reading source surface > Computing metric properties > Loading source values > mri_read(): couldn't determine type of file > /autofs/cluster/scratch/monday/raij/MEEG/AVL_GA_List1-00150.0-lh.w > ERROR: could not read AVL_GA_List1-00150.0-lh.w as type > > If I try to convert .w to .mgz I get the error > > mri_convert AVL_GA_List1-00150.0-lh.w AVL_GA_List1-00150.0-lh.mgz > > file not found or unknown file type for file AVL_GA_List1-00150.0-lh.w > > (which makes me think that perhaps the .w file from mne_analyze is > incompatible with much of FreeSurfer 5.1 code) > > Any suggestions? As always, thank you for the advice in advance! > > Best regards, > > 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 > > > -- 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 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.
