External Email - Use Caution
This is the actual command that fails:
mri_surfcluster --in rh.50to50.glmdir//con_nonpos/sig.mgh --mask
rh.50to50.glmdir//mask.mgh --cwsig
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.mgh --sum
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.summary --ocn
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.mgh --annot aparc
--cwpvalthresh .05 --o rh.50to50.glmdir//con_nonpos/--perm-resid.sig.masked.mgh
--no-fixmni --csd rh.50to50.glmdir//csd/--perm-resid.j001-con_nonpos.csd
--csdpdf rh.50to50.glmdir//con_nonpos/--perm-resid.pdf.dat --vwsig
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.voxel.mgh --vwsigmax
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.voxel.max.dat --oannot
rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.annot --surf white
Output is:
Creating CDFs from CSD files
csd->threshsign = 0
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
hemi = rh
srcid = rh.50to50.glmdir//con_nonpos/sig.mgh
srcsubjid = fsaverage
srcsurf = white
srcframe = 0
thsign = abs
thmin = 3
thmax = -1
fdr = -1
minarea = 0
xfmfile = talairach.xfm
nth = -1
outid = rh.50to50.glmdir//con_nonpos/--perm-resid.sig.masked.mgh MGH
ocnid = rh.50to50.glmdir//con_nonpos/--perm-resid.sig.ocn.mgh MGH
sumfile = rh.50to50.glmdir//con_nonpos/--perm-resid.sig.cluster.summary
subjectsdir = /usr/local/packages/freesurfer_v6.0.0/subjects
FixMNI = 0
Found 149926 vertices in mask
Found 149926 vertices in mask
Found 149926 points in clabel.
------------- 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;
MRISread(<D8>^Y$<91><FC>^?): could not open file
----------------------------------------------------
Reading source surface
/usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white
No such file or directory
mri_surfcluster: could not read surface
/usr/local/packages/freesurfer_v6.0.0/subjects/fsaverage/surf/rh.white
No such file or directory
When I removed the --vwsigmax option and ran the old version, it runs to
completion, and the following line:
MRISread(<D8>^Y$<91><FC>^?): could not open file
does not show up in the output.
-syam
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Syam Gadde
<syam.ga...@duke.edu>
Sent: Friday, March 27, 2020 11:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with
fspalm
External Email - Use Caution
Actually I was just sending an example command to demonstrate the same error.
I'll see if I can get the actual command fspalm was running.
-syam
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Friday, March 27, 2020 10:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Problem with version of mri_surfcluster provided with
fspalm
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://urldefense.com/v3/__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__;JSUlJSUlKysl!!OToaGQ!6icEV7Ijpg_iXl84kozP0KIV4fJUaOMqLJm_oi2GXBV86XgSCZYAPk2pXCLJTQMHJQ$
>
> 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
>
>
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