Hi Tommi, convert the w file to an mgz with mri_surf2surf. Specify the source format with --sfmt w doug
raij@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