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...
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