Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

[C.P.E. Rollins]

External Email - Use Caution

Hi Douglas,
Thanks for the response. Yes, I confirm that the file 
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can 
view it in freeview. Any other possible errors?
Also, would you mind elaborating how to use permutation to correct for 
MC for LGI? (as in what
to enter for command line?). I don't quite understand from the 
documentation.
Thanks again,
Colleen

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Freesurfer mailing list
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Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

[Greve, Douglas N.,Ph.D.]

can you verify that /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white 
exists and that you have read permission to it? Eg, can you load it with
freeview -f /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white




On 11/20/18 8:25 AM, C.P.E. Rollins wrote:
   External Email - Use Caution
Thanks Douglas, I've attached here the output from mri_glmfit-sim --glmdir 
lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug

Could you clarify how to use permutation to correct for MC for LGI? (as in what 
to enter for command line?). I don't quite understand from the documentation.

Thanks very much,
Colleen



set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return

goto check_params ;
goto check_params
if ( $#glmdir == 0 ) then
if ( 1 == 0 ) then
if ( $DoSim ) then
if ( 0 ) then
set residual = ( )
set residual = ( )
if ( $nulltype == perm && $PermResid ) then
if ( == perm && 1 ) then
if ( $DiagCluster && $DoBackground ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoPBSubmit ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoSim == 0 ) then
if ( 0 && 0 == 0 ) then

goto check_params_return ;
goto check_params_return

if ( ! -e $glmdir ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir ) then

set glmfitlog = $glmdir/mri_glmfit.log
set glmfitlog = lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( ! -e $glmfitlog ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/mri_glmfit.log ) then

if ( $nulltype != perm ) then
if ( != perm ) then
set fwhmfile = $glmdir/fwhm.dat
set fwhmfile = lh.5.lgi_MAN_new.glmdir/fwhm.dat
if ( ! -e $fwhmfile ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/fwhm.dat ) then

set fwhm = `cat $fwhmfile` ;
set fwhm = `cat $fwhmfile`
cat lh.5.lgi_MAN_new.glmdir/fwhm.dat
else
else

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( 0 && ! -e $glmfitcwd ) then
if ( 0 && ! -e /home/cper2/BeneMin/Freesurfer ) then
set glmfitcwd = `pwd` ;
set glmfitcwd = `pwd`
pwd

set anattype = volume ;
set anattype = volume
set subject = ( ) ;
set subject = ( )
set hemi = ( ) ;
set hemi = ( )
set surf = "white" ;
set surf = white
set wls = ( ) ;
set wls = ( )

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log


set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
awk {if($1 == "cmdline") print $0}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
set glmfitcmd = ( $glmfitcmd0 ) ;
set glmfitcmd = ( cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd 
FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt )
echo $glmfitcmd
echo cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods 
--glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
set gd2mtx = dods
set gd2mtx = dods
set UseTable = 0 ;
set UseTable = 0
set label = ( ) ;
set label = ( )
while ( $#glmfitcmd )
while ( 14 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = cmdline
shift glmfitcmd

switch ( $flag )
switch ( cmdline )
case "mri_glmfit"
case mri_glmfit
case "--prune"
case --prune
case "--no-prune"
case --no-prune
case "--pca"
case --pca
case "--synth"
case --synth
case "--allowsubjrep"
case --allowsubjrep
case "--illcond"
case --illcond
case "--debug"
case --debug
case "--synth"
case --synth
case "--cortex"
case --cortex
case "--kurtosis"
case --kurtosis
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
case "--rescale-x"
case --rescale-x
case "--no-rescale-x"
case --no-rescale-x
case "--fisher"
case --fisher
case "--no-pcc"
case --no-pcc
case "dods"
case dods
case "mri_glmfit.bin"
case mri_glmfit.bin
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 13 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = mri_glmfit.bin
shift glmfitcmd

switch ( $flag )
switch ( mri_glmfit.bin )
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 12 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --y
shift glmfitcmd

switch ( $flag )
switch ( --y )
if ( $#y == 0 ) set y = $glmfitcmd[1] ;
if ( 0 == 0 ) set y = lh.5.lgi_MAN_new.mgh
set y = lh.5.lgi_MAN_new.mgh
shift glmfitcmd ;
shift glmfitcmd
if ( $DoClusterMean ) then
if ( 1 ) then
if ( ! -e $y ) then
if ( ! -e lh.5.lgi_MAN_new.mgh ) then
endif
endif
if ( "$flag" == "--table" ) set UseTable = 1 ;
if ( --y == --table ) set UseTable = 1
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 10 )
set flag = $glmfitcmd[1] ;

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

[C.P.E. Rollins]

   External Email - Use Caution

Thanks Douglas, I've attached here the output from mri_glmfit-sim 
--glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces 
--debug


Could you clarify how to use permutation to correct for MC for LGI? (as 
in what to enter for command line?). I don't quite understand from the 
documentation.


Thanks very much,
Colleenset echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return

goto check_params ;
goto check_params
if ( $#glmdir == 0 ) then
if ( 1 == 0 ) then
if ( $DoSim ) then
if ( 0 ) then
set residual = ( )
set residual = ( )
if ( $nulltype == perm && $PermResid ) then
if ( == perm && 1 ) then
if ( $DiagCluster && $DoBackground ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoPBSubmit ) then
if ( 0 && 0 ) then
if ( $DiagCluster && $DoSim == 0 ) then
if ( 0 && 0 == 0 ) then

goto check_params_return ;
goto check_params_return

if ( ! -e $glmdir ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir ) then

set glmfitlog = $glmdir/mri_glmfit.log
set glmfitlog = lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( ! -e $glmfitlog ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/mri_glmfit.log ) then

if ( $nulltype != perm ) then
if ( != perm ) then
set fwhmfile = $glmdir/fwhm.dat
set fwhmfile = lh.5.lgi_MAN_new.glmdir/fwhm.dat
if ( ! -e $fwhmfile ) then
if ( ! -e lh.5.lgi_MAN_new.glmdir/fwhm.dat ) then

set fwhm = `cat $fwhmfile` ;
set fwhm = `cat $fwhmfile`
cat lh.5.lgi_MAN_new.glmdir/fwhm.dat
else
else

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
if ( 0 && ! -e $glmfitcwd ) then
if ( 0 && ! -e /home/cper2/BeneMin/Freesurfer ) then
set glmfitcwd = `pwd` ;
set glmfitcwd = `pwd`
pwd

set anattype = volume ;
set anattype = volume
set subject = ( ) ;
set subject = ( )
set hemi = ( ) ;
set hemi = ( )
set surf = "white" ;
set surf = white
set wls = ( ) ;
set wls = ( )

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`
awk {if($1 == "cwd") print $2}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log


set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`
awk {if($1 == "cmdline") print $0}
cat lh.5.lgi_MAN_new.glmdir/mri_glmfit.log
set glmfitcmd = ( $glmfitcmd0 ) ;
set glmfitcmd = ( cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd 
FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt )
echo $glmfitcmd
echo cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods 
--glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt
set gd2mtx = dods
set gd2mtx = dods
set UseTable = 0 ;
set UseTable = 0
set label = ( ) ;
set label = ( )
while ( $#glmfitcmd )
while ( 14 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = cmdline
shift glmfitcmd

switch ( $flag )
switch ( cmdline )
case "mri_glmfit"
case mri_glmfit
case "--prune"
case --prune
case "--no-prune"
case --no-prune
case "--pca"
case --pca
case "--synth"
case --synth
case "--allowsubjrep"
case --allowsubjrep
case "--illcond"
case --illcond
case "--debug"
case --debug
case "--synth"
case --synth
case "--cortex"
case --cortex
case "--kurtosis"
case --kurtosis
case "--nii"
case --nii
case "--nii.gz"
case --nii.gz
case "--rescale-x"
case --rescale-x
case "--no-rescale-x"
case --no-rescale-x
case "--fisher"
case --fisher
case "--no-pcc"
case --no-pcc
case "dods"
case dods
case "mri_glmfit.bin"
case mri_glmfit.bin
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 13 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = mri_glmfit.bin
shift glmfitcmd

switch ( $flag )
switch ( mri_glmfit.bin )
case "--save-eres"
case --save-eres
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 12 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --y
shift glmfitcmd

switch ( $flag )
switch ( --y )
if ( $#y == 0 ) set y = $glmfitcmd[1] ;
if ( 0 == 0 ) set y = lh.5.lgi_MAN_new.mgh
set y = lh.5.lgi_MAN_new.mgh
shift glmfitcmd ;
shift glmfitcmd
if ( $DoClusterMean ) then
if ( 1 ) then
if ( ! -e $y ) then
if ( ! -e lh.5.lgi_MAN_new.mgh ) then
endif
endif
if ( "$flag" == "--table" ) set UseTable = 1 ;
if ( --y == --table ) set UseTable = 1
breaksw
breaksw
end
end
while ( $#glmfitcmd )
while ( 10 )
set flag = $glmfitcmd[1] ; shift glmfitcmd ;
set flag = --fsgd
shift glmfitcmd

switch ( $flag )
switch ( --fsgd )
shift glmfitcmd ;
shift glmfitcmd
if ( $#glmfitcmd > 0 ) then
if ( 8 > 0 ) then
if ( $glmfitcmd[1] == doss ) set gd2mtx = doss
if ( dods == doss ) set gd2mtx = doss

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

[Greve, Douglas N.,Ph.D.]

I can' tell what is going wrong there. Can you run it with --debug as 
the first option and send the output? BTW, the MC correction for LGI is 
probably not very accurate. I would recommend using permutation. See 
here 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsClusterSummaryV6.0Perm


On 11/19/18 7:17 AM, C.P.E. Rollins wrote:
>  External Email - Use Caution
>
> Dear Freesurfer Developers,
>
> I'm trying to run mri_glmfit-sim to correct for multiple comparisons but
> am receiving the following error:
>
> cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt
> dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C
> contrast_dods.txt
> SURFACE: fsaverage lh
> log file is lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log
>
> cd /home/cper2/BeneMin/Freesurfer
> /applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim
> --glmdir lh.5.lgi_MAN_new.glmdir --cache 2 neg --cwp 0.05 --2spaces
>
> $Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $
> Fri Nov 16 09:38:40 GMT 2018
> Linux wbic-gate-2 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14)
> x86_64 GNU/Linux
> cper2
> setenv SUBJECTS_DIR /home/cper2/BeneMin/Freesurfer
> FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0
>
> Original mri_glmfit command line:
> cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt
> dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C
> contrast_dods.txt
>
> DoSim = 0
> UseCache = 1
> DoPoll = 0
> DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = dods
> fwhm = 26.134985
> CSD
> /applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd
> mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh
> --mask lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.mgh
> --sum
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary
> --ocn
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh
> --annot aparc --cwpvalthresh 0.05 --o
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh
> --no-fixmni --csd
> /applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd
> --csdpdf
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.pdf.dat --vwsig
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.mgh
> --vwsigmax
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.max.dat
> --oannot
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.annot
> --bonferroni 2 --surf white
> Creating CDFs from CSD files
> csd->threshsign = -1
> thsign = neg, id = -1
> version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
> hemi   = lh
> srcid  = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh
> srcsubjid  = fsaverage
> srcsurf= white
> srcframe   = 0
> thsign = neg
> thmin  = 2
> thmax  = -1
> fdr= -1
> minarea= 0
> Bonferroni  = 2
> xfmfile= talairach.xfm
> nth = -1
> outid=
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh
> MGH
> ocnid=
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh MGH
> sumfile  =
> lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary
> subjectsdir= /home/cper2/BeneMin/Freesurfer
> FixMNI = 0
> Found 149955 vertices in mask
> Found 149955 vertices in mask
> Found 149955 points in clabel.
> - XFM matrix (RAS2RAS) ---
> /home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm
>1.0   0.0   0.0   0.0;
>0.0   1.0   0.0   0.0;
>0.0   0.0   1.0   0.0;
>0.0   0.0   0.0   1.0;
> MRISread(?): could not open file
> No such file or directory
> 
> Reading source surface
> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
> mri_surfcluster.bin: could not read surface
> /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
> No such file or directory
>
> However, the files
> /home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm
> and /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white both exist
> and I can read them looking at the permissions.
>
> I was wondering if you might have any advice for this.
>
> Many thanks,
> Colleen
>
> ___
> 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

[Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

[C.P.E. Rollins]

External Email - Use Caution

Dear Freesurfer Developers,

I'm trying to run mri_glmfit-sim to correct for multiple comparisons but 
am receiving the following error:

cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt
SURFACE: fsaverage lh
log file is lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log

cd /home/cper2/BeneMin/Freesurfer
/applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim
--glmdir lh.5.lgi_MAN_new.glmdir --cache 2 neg --cwp 0.05 --2spaces

$Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $
Fri Nov 16 09:38:40 GMT 2018
Linux wbic-gate-2 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) 
x86_64 GNU/Linux
cper2
setenv SUBJECTS_DIR /home/cper2/BeneMin/Freesurfer
FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0

Original mri_glmfit command line:
cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt 
dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C 
contrast_dods.txt

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 26.134985
CSD 
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd
mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh 
--mask lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.mgh 
--sum 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary 
--ocn 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh 
--annot aparc --cwpvalthresh 0.05 --o 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh 
--no-fixmni --csd 
/applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd
 
--csdpdf 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.pdf.dat --vwsig 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.mgh 
--vwsigmax 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.max.dat 
--oannot 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.annot 
--bonferroni 2 --surf white
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $
hemi   = lh
srcid  = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 2
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh 
MGH
ocnid= 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh MGH
sumfile  = 
lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary
subjectsdir= /home/cper2/BeneMin/Freesurfer
FixMNI = 0
Found 149955 vertices in mask
Found 149955 vertices in mask
Found 149955 points in clabel.
- XFM matrix (RAS2RAS) ---
/home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm
  1.0   0.0   0.0   0.0;
  0.0   1.0   0.0   0.0;
  0.0   0.0   1.0   0.0;
  0.0   0.0   0.0   1.0;
MRISread(?): could not open file
No such file or directory

Reading source surface 
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
mri_surfcluster.bin: could not read surface 
/home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white
No such file or directory

However, the files 
/home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm 
and /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white both exist 
and I can read them looking at the permissions.

I was wondering if you might have any advice for this.

Many thanks,
Colleen

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