Hi Syam, it looks like fspalm is not creating the correct command line for mri_surfcluster (the --in should be an output of palm, not the fsaverage surface). Can you send the full terminal output? doug
On 3/25/2020 9:13 AM, Syam Gadde wrote: > External Email - Use Caution > > Hi, > > We have a user trying to use fspalm. I followed all the directions to > install, but are getting an error with the new mri_surfcluster that we were > asked to download with fspalm. Here is the dummy command I ran to replicate > the error: > > mri_surfcluster --thmin 0 --subject fsaverage --hemi lh --in > /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white > > and the end of its output: > > <...> > subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects > FixMNI = 1 > ------------- XFM matrix (RAS2RAS) --------------- > /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/mri/transforms/talairach.xfm > 1.00000 0.00000 0.00000 0.00000; > 0.00000 1.00000 0.00000 0.00000; > 0.00000 0.00000 1.00000 0.00000; > 0.00000 0.00000 0.00000 1.00000; > ---------------------------------------------------- > Reading source surface > /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white > MRISread(x�<m�): could not open file > No such file or directory > mri_surfcluster: could not read surface > /usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/lh.white > No such file or directory > ----- > > It is the same error reported in these emails: > > https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+mri_surfcluster+ERROR%22&o=newest > > but the error message is misleading. The problem is not in reading the > surface file, but in trying to read a file name made up of non-ascii (or > presumably unicode) characters. As shown by strace: > > ... > read(3, "", 8192) = 0 > open("/proc/sys/crypto/fips_enabled", O_RDONLY) = 4 > read(4, "0\n", 31) = 2 > close(4) = 0 > close(3) = 0 > munmap(0x7f8413571000, 8192) = 0 > open("\310\215\26\f\376\177", O_RDONLY) = -1 ENOENT (No such file or > directory) > write(2, "MRISread(\310\215\26\f\376\177): could not open"..., > 37MRISread(ȍ^V^L<FE>^?): c > ould not open file) = 37 > ... > > Any thoughts on how to proceed? Thanks, > > -syam > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
