Hi Doug, I am still receiving a similar error. mri_surf2surf inputes the w file and writes out a mgz file and exits apparently ok. However, mri_volcluster still exits with "could not read test-lh.mgz as type"
Details: mri_surf2surf \ --srcsubject Wyss_000 \ --trgsubject Wyss_000 \ --hemi lh \ --srcsurfval AVL_GA_List1-00150.0-lh.w \ --trgsurfval test.lh.mgz \ --sfmt w \ --tfmt mgz \ srcsubject = Wyss_000 srcval = AVL_GA_List1-00150.0-lh.w srctype = w trgsubject = Wyss_000 trgval = test.lh.mgz trgtype = mgz srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /cluster/scratch/monday/raij/MRIs/Wyss_000/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to test.lh.mgz mri_surfcluster --subject Wyss_000 --hemi lh --in test-lh.mgz --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 = test-lh.mgz 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 mghRead(/autofs/cluster/scratch/monday/raij/MEEG/test-lh.mgz, -1): could not open file ERROR: could not read test-lh.mgz as type -Tommi > 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. 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