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Hello Freesurfer Developpers,
I'm trying to use mri_glmfit-sim to make clusterwise corrections but am
running into the following error:
------------- XFM matrix (RAS2RAS) ---------------
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/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('\ufffd\ufffd): could not open file
No such file or directory
----------------------------------------------------
Reading source surface
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
mri_surfcluster.bin: could not read surface
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
No such file or directory
I've attached here the log file. I was wondering if you had any insights
into the error?
Thanks a lot for your help.
Colleen
cd /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
/applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim
--glmdir rh.10.thickness.glmdir --cache 2 abs --cwp 0.05 --2spaces
$Id: mri_glmfit-sim,v 1.60.2.4 2016/11/17 18:01:28 zkaufman Exp $
Fri Sep 21 16:21:47 BST 2018
Linux wbic-gate-1 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64
GNU/Linux
cper2
setenv SUBJECTS_DIR /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
Original mri_glmfit command line:
cmdline mri_glmfit.bin --y rh.10.thickness.post.mgh --fsgd FSGD.txt doss --C
contrast_doss.txt --surf fsaverage rh --cortex --glmdir rh.10.thickness.glmdir
DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = doss
fwhm = 14.003044
CSD
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/rh/cortex/fwhm14/abs/th20/mc-z.csd
mri_surfcluster --in rh.10.thickness.glmdir/contrast_doss.txt/sig.mgh --mask
rh.10.thickness.glmdir/mask.mgh --cwsig
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.cluster.mgh --sum
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.cluster.summary
--ocn rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.masked.mgh
--no-fixmni --csd
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/rh/cortex/fwhm14/abs/th20/mc-z.csd
--csdpdf rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.pdf.dat
--vwsig rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.voxel.mgh
--vwsigmax
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.voxel.max.dat
--oannot rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.ocn.annot
--bonferroni 2 --surf white
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.10.thickness.glmdir/contrast_doss.txt/sig.mgh
srcsubjid = fsaverage
srcsurf = white
srcframe = 0
thsign = abs
thmin = 2
thmax = -1
fdr = -1
minarea = 0
Bonferroni = 2
xfmfile = talairach.xfm
nth = -1
outid =
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.masked.mgh MGH
ocnid = rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.ocn.mgh
MGH
sumfile =
rh.10.thickness.glmdir/contrast_doss.txt/cache.th20.abs.sig.cluster.summary
subjectsdir = /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer
FixMNI = 0
Found 148285 vertices in mask
Found 148285 vertices in mask
Found 148285 points in clabel.
------------- XFM matrix (RAS2RAS) ---------------
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/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
/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white
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