mri_glmfit-sim ERROR cannot find mc-z.csd file

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Re: [Freesurfer] UPDATE: Matlab...

Aly Negreira

1 Jul 2017 1 Jul '17

1:57 p.m.

Hi Freesurfer Community,

I'm using FsFast on my dissertation data and trying to run a monte carlo correction on my functional data in the volume. I keep running into the below error. In attempting to troubleshoot, it looks like Yuko ran into a similiar issue (see archived email from Fri Dec 9 @ 12:26:46 EST in 2011) just not sure how to fix it! Please advice....I just want my PhD already!

Thank you!

Aly

ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd COMMAND: mri_glmfit-sim \ --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ \ --cache 1.3 abs \ --cwp 0.05\ --3spaces

MAC INFO: OS X El Capitan Version 10.11.6

FREESURFER VERSION: -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------

Attachments:

attachment.html (text/html — 1.2 KB)

Show replies by date

Douglas Greve

7 Jul 7 Jul

2:15 p.m.

Hi Aly, it is not creating the path correctly, not sure why. Can you run it again with --debug as the first option and send me the terminal output?

doug

On 7/1/17 1:57 PM, Aly Negreira wrote:

...

Hi Freesurfer Community,

I'm using FsFast on my dissertation data and trying to run a monte carlo correction on my functional data in the volume. I keep running into the below error. In attempting to troubleshoot, it looks like Yuko ran into a similiar issue (see archived email from Fri Dec 9 @ 12:26:46 EST in 2011) just not sure how to fix it! Please advice....I just want my PhD already!

Thank you!

Aly

ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd COMMAND: mri_glmfit-sim \ --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ \ --cache 1.3 abs \ --cwp 0.05\ --3spaces

MAC INFO: OS X El Capitan Version 10.11.6

FREESURFER VERSION: -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Aly Negreira

8 Jul 8 Jul

1:03 p.m.

Hi Doug!

Thank you for the reply! Re-ran w/ --debug as first option. Below is the output. Not sure if this is helpful, but when I cd to /Applications/freesurfer/average/mult-comp-cor/fsaverage there are only directories for lh and rh, nothing for mni.

Thanks for the help!

Aly

Alysons-iMac:~/analyses/EMOT_REG_FX_DISS] aneg% mri_glmfit-sim \ --debug \

--glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ \

--cache 1.3 abs \

--cwp 0.05\

--3spaces ? --debug \

? --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ \

? --cache 1.3 abs \

? --cwp 0.05\

? --3spaces \

set echo = 1 ;

breaksw

end

while ( $#argv != 0 )

while ( 8 != 0 )

set flag = $argv[1] ; shift ;

set flag = --glmdir

shift

switch ( $flag )

switch ( --glmdir )

if ( $#argv < 0 ) goto arg1err ;

if ( 7 < 0 ) goto arg1err

set glmdir = $argv[1] ; shift ;

set glmdir = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/

shift

breaksw

end

while ( $#argv != 0 )

while ( 6 != 0 )

set flag = $argv[1] ; shift ;

set flag = --cache

shift

switch ( $flag )

switch ( --cache )

if ( $#argv < 2 ) goto arg2err ;

if ( 5 < 2 ) goto arg2err

set thresh = $argv[1] ; shift ;

set thresh = 1.3

shift

set simsign = $argv[1] ; shift ;

set simsign = abs

shift

set UseCache = 1 ;

set UseCache = 1

set DoSim = 0 ;

set DoSim = 0

set thresh = `printf %2.1f $thresh`

printf %2.1f 1.3

if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then

if ( 1.3 != 1.3 && 1.3 != 2.0 && 1.3 != 2.3 && 1.3 != 3.0 && 1.3 != 3.3 && 1.3 != 4.0 ) then

breaksw

end

while ( $#argv != 0 )

while ( 3 != 0 )

set flag = $argv[1] ; shift ;

set flag = --cwp

shift

switch ( $flag )

switch ( --cwp )

case "--cwpvalthresh":

case --cwpvalthresh:

if ( $#argv < 1 ) goto arg1err ;

if ( 2 < 1 ) goto arg1err

set cwpvalthresh = $argv[1] ; shift ;

set cwpvalthresh = 0.05

shift

breaksw

end

while ( $#argv != 0 )

while ( 1 != 0 )

set flag = $argv[1] ; shift ;

set flag = --3spaces

shift

switch ( $flag )

switch ( --3spaces )

set Bonferroni = 3 ;

set Bonferroni = 3

breaksw

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

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 GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ ) then

set glmfitlog = $glmdir/mri_glmfit.log

set glmfitlog = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

if ( ! -e $glmfitlog ) then

if ( ! -e GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log ) then

set mask = `stem2fname $glmdir/mask`

stem2fname GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mask

if ( $status ) then

if ( 0 ) then

if ( $nulltype != perm ) then

if ( != perm ) then

set fwhmfile = $glmdir/fwhm.dat

set fwhmfile = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat

if ( ! -e $fwhmfile ) then

if ( ! -e GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat ) then

set fwhm = `cat $fwhmfile` ;

set fwhm = `cat $fwhmfile`

cat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat

else

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`

cat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

awk {if($1 == "cwd") print $2}

if ( ! -e $glmfitcwd ) then

if ( ! -e /Users/aneg/analyses/EMOT_REG_FX_DISS ) then

set anattype = volume ;

set anattype = volume

set subject = ( ) ;

set subject = ( )

set hemi = ( ) ;

set hemi = ( )

set surf = "white" ;

set surf = white

set y = ( ) ;

set y = ( )

set wls = ( ) ;

set wls = ( )

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`

cat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

awk {if($1 == "cwd") print $2}

set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`

cat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

awk {if($1 == "cmdline") print $0}

set glmfitcmd = ( $glmfitcmd0 ) ;

set glmfitcmd = ( cmdline mri_glmfit --y GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz --wls GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz --osgm --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --nii.gz )

echo $glmfitcmd

echo cmdline mri_glmfit --y GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz --wls GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz --osgm --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --nii.gz

cmdline mri_glmfit --y GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz --wls GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz --osgm --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --nii.gz

set gd2mtx = dods

set label = ( ) ;

set label = ( )

while ( $#glmfitcmd )

while ( 10 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = cmdline

shift glmfitcmd

switch ( $flag )

switch ( cmdline )

case "mri_glmfit"

case mri_glmfit

case "--osgm"

case --osgm

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 "dods"

case dods

breaksw

end

while ( $#glmfitcmd )

while ( 9 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = mri_glmfit

shift glmfitcmd

switch ( $flag )

switch ( mri_glmfit )

case "--osgm"

case --osgm

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 "dods"

case dods

breaksw

end

while ( $#glmfitcmd )

while ( 8 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --y

shift glmfitcmd

switch ( $flag )

switch ( --y )

set y = $glmfitcwd/$glmfitcmd[1] ; shift glmfitcmd ;

set y = /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz

shift glmfitcmd

if ( ! -e $y ) then

if ( ! -e /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz ) then

breaksw

end

while ( $#glmfitcmd )

while ( 6 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --wls

shift glmfitcmd

switch ( $flag )

switch ( --wls )

set wls = $glmfitcwd/$glmfitcmd[1] ; shift glmfitcmd ;

set wls = /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz

shift glmfitcmd

if ( ! -e $wls ) then

if ( ! -e /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz ) then

breaksw

end

while ( $#glmfitcmd )

while ( 4 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --osgm

shift glmfitcmd

switch ( $flag )

switch ( --osgm )

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 "dods"

case dods

breaksw

end

while ( $#glmfitcmd )

while ( 3 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --glmdir

shift glmfitcmd

switch ( $flag )

switch ( --glmdir )

case "--o"

case --o

case "--C"

case --C

case "--X"

case --X

case "--w"

case --w

case "--fwhm"

case --fwhm

case "--mask"

case --mask

case "--seed"

case --seed

case "--var-fwhm"

case --var-fwhm

case "--yffxvar"

case --yffxvar

case "--ffxdof"

case --ffxdof

case "--ffxdofdat"

case --ffxdofdat

shift glmfitcmd ;

shift glmfitcmd

breaksw

end

while ( $#glmfitcmd )

while ( 1 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --nii.gz

shift glmfitcmd

switch ( $flag )

switch ( --nii.gz )

case "--rescale-x"

case --rescale-x

case "--no-rescale-x"

case --no-rescale-x

case "dods"

case dods

breaksw

end

while ( $#glmfitcmd )

while ( 0 )

if ( $UseGRF && $anattype != volume ) then

if ( 0 && volume != volume ) then

if ( $UseGRF ) then

if ( 0 ) then

if ( $#subjectOverride ) set subject = $subjectOverride

if ( 0 ) set subject =

if ( $#subject != 0 ) then

if ( 0 != 0 ) then

if ( $#tmpdir == 0 ) set tmpdir = $glmdir/tmp.mri_glmfit-sim-$$

if ( 0 == 0 ) set tmpdir = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128

set tmpdir = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128

mkdir -p $tmpdir

mkdir -p GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128

set clist = ( $glmdir/*/C.dat )

set clist = ( GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//*/C.dat )

if ( $status ) then

if ( 0 ) then

set clist2 = ( ) ;

set clist2 = ( )

set conlist = ( ) ;

set conlist = ( )

foreach c ( $clist )

foreach c ( GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat )

set tmp = `dirname $c`

dirname GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat

set conname = `basename $tmp`

basename GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm

set conlist = ( $conlist $conname ) ;

set conlist = ( osgm )

set confile = $tmpdir/$conname.mtx

set confile = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx

cp $c $confile

cp GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx

set clist2 = ( $clist2 --C $confile ) ;

set clist2 = ( --C GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx )

set sig = `stem2fname $glmdir/$conname/sig`

stem2fname GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/sig

if ( $status ) then

if ( 0 ) then

if ( $DoSim ) then

if ( 0 ) then

end

set StartDate = `date`

date

if ( $#LF == 0 ) then

if ( 0 == 0 ) then

if ( $UseCache == 0 ) then

if ( 1 == 0 ) then

set LF = $glmdir/cache.mri_glmfit-sim.log

set LF = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

endif

rm -f $LF

rm -f GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

endif

echo "log file is $LF"

echo log file is GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

log file is GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo "" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo

echo "cd `pwd`" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo cd `pwd`

pwd

cd /Users/aneg/analyses/EMOT_REG_FX_DISS

echo $0 | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo /Applications/freesurfer/bin/mri_glmfit-sim

/Applications/freesurfer/bin/mri_glmfit-sim

echo $inputargs | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo --debug --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --cache 1.3 abs --cwp 0.05 --3spaces

--debug --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --cache 1.3 abs --cwp 0.05 --3spaces

echo "" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo

echo $VERSION | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $

date | tee -a $LF

date

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

Sat Jul 8 12:57:27 EDT 2017

uname -a | tee -a $LF

uname -a

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

Darwin Alysons-iMac.local 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64

echo $user | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo aneg

aneg

echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo setenv SUBJECTS_DIR /Users/aneg/analyses/EMOT_REG_RECON_DISS

setenv SUBJECTS_DIR /Users/aneg/analyses/EMOT_REG_RECON_DISS

echo "FREESURFER_HOME $FREESURFER_HOME" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo FREESURFER_HOME /Applications/freesurfer

FREESURFER_HOME /Applications/freesurfer

echo "" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo

echo "Original mri_glmfit command line:" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo Original mri_glmfit command line:

Original mri_glmfit command line:

echo $glmfitcmd0 | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo "" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo

echo "DoSim = $DoSim" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoSim = 0

DoSim = 0

echo "UseCache = $UseCache" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo UseCache = 1

UseCache = 1

echo "DoPoll = $DoPoll" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoPoll = 0

DoPoll = 0

echo "DoPBSubmit = $DoPBSubmit" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoPBSubmit = 0

DoPBSubmit = 0

echo "DoBackground = $DoBackground" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoBackground = 0

DoBackground = 0

echo "DiagCluster = $DiagCluster" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DiagCluster = 0

DiagCluster = 0

echo "gd2mtx = $gd2mtx" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo gd2mtx = dods

gd2mtx = dods

if ( $#Seed ) echo "Seed = $Seed" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

if ( 0 ) echo Seed =

echo "fwhm = $fwhm" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo fwhm = 9.625207

fwhm = 9.625207

if ( $#fwhmOverride ) then

if ( 0 ) then

if ( $UseCache ) then

if ( 1 ) then

set fwhm = `cat $glmdir/fwhm.dat` ;

set fwhm = `cat $glmdir/fwhm.dat`

cat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat

set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+.5 ) ) "`

perl -e printf('%02d',int ( 9.625207+.5 ) )

set threshStr = `perl -e "print 10*$thresh"` ;

set threshStr = `perl -e "print 10*$thresh"`

perl -e print 10*1.3

set csdCache = $CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd

set csdCache = /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd

if ( ! -e $csdCache ) then

if ( ! -e /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd ) then

echo "ERROR: cannot find $csdCache" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd

ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd

exit 1 ;

exit 1

Douglas N Greve

12 Jul 12 Jul

12:17 p.m.

Is this for a volume analysis? If so, then you'll need to use the --grf option instead of using the mcz simulations (those are just for surface)

On 07/08/2017 01:03 PM, Aly Negreira wrote:

...

Hi Doug!

Thank you for the reply! Re-ran w/ --debug as first option. Below is the output. Not sure if this is helpful, but when I cd to /Applications/freesurfer/average/mult-comp-cor/fsaverage there are only directories for lh and rh, nothing for mni.

Thanks for the help!

Aly

Alysons-iMac:~/analyses/EMOT_REG_FX_DISS] aneg% mri_glmfit-sim \ --debug \

--glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ \

--cache 1.3 abs \

--cwp 0.05\

--3spaces ? --debug \

? --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ \

? --cache 1.3 abs \

? --cwp 0.05\

? --3spaces \

?

set echo = 1 ;

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 8 != 0 )

set flag = $argv[1] ; shift ;

set flag = --glmdir

shift

switch ( $flag )

switch ( --glmdir )

if ( $#argv < 0 ) goto arg1err ;

if ( 7 < 0 ) goto arg1err

set glmdir = $argv[1] ; shift ;

set glmdir = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/

shift

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 6 != 0 )

set flag = $argv[1] ; shift ;

set flag = --cache

shift

switch ( $flag )

switch ( --cache )

if ( $#argv < 2 ) goto arg2err ;

if ( 5 < 2 ) goto arg2err

set thresh = $argv[1] ; shift ;

set thresh = 1.3

shift

set simsign = $argv[1] ; shift ;

set simsign = abs

shift

set UseCache = 1 ;

set UseCache = 1

set DoSim = 0 ;

set DoSim = 0

set thresh = `printf %2.1f $thresh`

set thresh = `printf %2.1f $thresh`

printf %2.1f 1.3

if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then

if ( 1.3 != 1.3 && 1.3 != 2.0 && 1.3 != 2.3 && 1.3 != 3.0 && 1.3 != 3.3 && 1.3 != 4.0 ) then

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 3 != 0 )

set flag = $argv[1] ; shift ;

set flag = --cwp

shift

switch ( $flag )

switch ( --cwp )

case "--cwpvalthresh":

case --cwpvalthresh:

if ( $#argv < 1 ) goto arg1err ;

if ( 2 < 1 ) goto arg1err

set cwpvalthresh = $argv[1] ; shift ;

set cwpvalthresh = 0.05

shift

breaksw

breaksw

end

end

while ( $#argv != 0 )

while ( 1 != 0 )

set flag = $argv[1] ; shift ;

set flag = --3spaces

shift

switch ( $flag )

switch ( --3spaces )

set Bonferroni = 3 ;

set Bonferroni = 3

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

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 GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ ) then

set glmfitlog = $glmdir/mri_glmfit.log

set glmfitlog = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

if ( ! -e $glmfitlog ) then

if ( ! -e GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log ) then

set mask = `stem2fname $glmdir/mask`

set mask = `stem2fname $glmdir/mask`

stem2fname GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mask

if ( $status ) then

if ( 0 ) then

if ( $nulltype != perm ) then

if ( != perm ) then

set fwhmfile = $glmdir/fwhm.dat

set fwhmfile = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat

if ( ! -e $fwhmfile ) then

if ( ! -e GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat ) then

set fwhm = `cat $fwhmfile` ;

set fwhm = `cat $fwhmfile`

cat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat

else

else

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`

cat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

awk {if($1 == "cwd") print $2}

if ( ! -e $glmfitcwd ) then

if ( ! -e /Users/aneg/analyses/EMOT_REG_FX_DISS ) then

set anattype = volume ;

set anattype = volume

set subject = ( ) ;

set subject = ( )

set hemi = ( ) ;

set hemi = ( )

set surf = "white" ;

set surf = white

set y = ( ) ;

set y = ( )

set wls = ( ) ;

set wls = ( )

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`

set glmfitcwd = `cat $glmfitlog | awk '{if($1 == "cwd") print $2}'`

cat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

awk {if($1 == "cwd") print $2}

set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`

set glmfitcmd0 = `cat $glmfitlog | awk '{if($1 == "cmdline") print $0}'`

cat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//mri_glmfit.log

awk {if($1 == "cmdline") print $0}

set glmfitcmd = ( $glmfitcmd0 ) ;

set glmfitcmd = ( cmdline mri_glmfit --y GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz --wls GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz --osgm --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --nii.gz )

echo $glmfitcmd

echo cmdline mri_glmfit --y GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz --wls GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz --osgm --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --nii.gz

cmdline mri_glmfit --y GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz --wls GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz --osgm --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --nii.gz

set gd2mtx = dods

set gd2mtx = dods

set label = ( ) ;

set label = ( )

while ( $#glmfitcmd )

while ( 10 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = cmdline

shift glmfitcmd

switch ( $flag )

switch ( cmdline )

case "mri_glmfit"

case mri_glmfit

case "--osgm"

case --osgm

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 "dods"

case dods

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 9 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = mri_glmfit

shift glmfitcmd

switch ( $flag )

switch ( mri_glmfit )

case "--osgm"

case --osgm

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 "dods"

case dods

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 8 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --y

shift glmfitcmd

switch ( $flag )

switch ( --y )

set y = $glmfitcwd/$glmfitcmd[1] ; shift glmfitcmd ;

set y = /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz

shift glmfitcmd

if ( ! -e $y ) then

if ( ! -e /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz ) then

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 6 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --wls

shift glmfitcmd

switch ( $flag )

switch ( --wls )

set wls = $glmfitcwd/$glmfitcmd[1] ; shift glmfitcmd ;

set wls = /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz

shift glmfitcmd

if ( ! -e $wls ) then

if ( ! -e /Users/aneg/analyses/EMOT_REG_FX_DISS/GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz ) then

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 4 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --osgm

shift glmfitcmd

switch ( $flag )

switch ( --osgm )

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 "dods"

case dods

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 3 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --glmdir

shift glmfitcmd

switch ( $flag )

switch ( --glmdir )

case "--o"

case --o

case "--C"

case --C

case "--X"

case --X

case "--w"

case --w

case "--fwhm"

case --fwhm

case "--mask"

case --mask

case "--seed"

case --seed

case "--var-fwhm"

case --var-fwhm

case "--yffxvar"

case --yffxvar

case "--ffxdof"

case --ffxdof

case "--ffxdofdat"

case --ffxdofdat

shift glmfitcmd ;

shift glmfitcmd

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 1 )

set flag = $glmfitcmd[1] ; shift glmfitcmd ;

set flag = --nii.gz

shift glmfitcmd

switch ( $flag )

switch ( --nii.gz )

case "--rescale-x"

case --rescale-x

case "--no-rescale-x"

case --no-rescale-x

case "dods"

case dods

breaksw

breaksw

end

end

while ( $#glmfitcmd )

while ( 0 )

if ( $UseGRF && $anattype != volume ) then

if ( 0 && volume != volume ) then

if ( $UseGRF ) then

if ( 0 ) then

if ( $#subjectOverride ) set subject = $subjectOverride

if ( 0 ) set subject =

if ( $#subject != 0 ) then

if ( 0 != 0 ) then

if ( $#tmpdir == 0 ) set tmpdir = $glmdir/tmp.mri_glmfit-sim-$$

if ( 0 == 0 ) set tmpdir = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128

set tmpdir = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128

mkdir -p $tmpdir

mkdir -p GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128

set clist = ( $glmdir/*/C.dat )

set clist = ( GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//*/C.dat )

if ( $status ) then

if ( 0 ) then

set clist2 = ( ) ;

set clist2 = ( )

set conlist = ( ) ;

set conlist = ( )

foreach c ( $clist )

foreach c ( GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat )

set tmp = `dirname $c`

set tmp = `dirname $c`

dirname GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat

set conname = `basename $tmp`

set conname = `basename $tmp`

basename GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm

set conlist = ( $conlist $conname ) ;

set conlist = ( osgm )

set confile = $tmpdir/$conname.mtx

set confile = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx

cp $c $confile

cp GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/C.dat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx

set clist2 = ( $clist2 --C $confile ) ;

set clist2 = ( --C GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//tmp.mri_glmfit-sim-21128/osgm.mtx )

set sig = `stem2fname $glmdir/$conname/sig`

set sig = `stem2fname $glmdir/$conname/sig`

stem2fname GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//osgm/sig

if ( $status ) then

if ( 0 ) then

if ( $DoSim ) then

if ( 0 ) then

end

end

set StartDate = `date`

set StartDate = `date`

date

if ( $#LF == 0 ) then

if ( 0 == 0 ) then

if ( $UseCache == 0 ) then

if ( 1 == 0 ) then

set LF = $glmdir/cache.mri_glmfit-sim.log

set LF = GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

endif

endif

rm -f $LF

rm -f GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

endif

endif

echo "log file is $LF"

echo log file is GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

log file is GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo "" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo

echo "cd `pwd`" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo cd `pwd`

pwd

cd /Users/aneg/analyses/EMOT_REG_FX_DISS

echo $0 | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo /Applications/freesurfer/bin/mri_glmfit-sim

/Applications/freesurfer/bin/mri_glmfit-sim

echo $inputargs | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo --debug --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --cache 1.3 abs --cwp 0.05 --3spaces

--debug --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --cache 1.3 abs --cwp 0.05 --3spaces

echo "" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo

echo $VERSION | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $

date | tee -a $LF

date

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

Sat Jul 8 12:57:27 EDT 2017

uname -a | tee -a $LF

uname -a

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

Darwin Alysons-iMac.local 15.6.0 Darwin Kernel Version 15.6.0: Tue Apr 11 16:00:51 PDT 2017; root:xnu-3248.60.11.5.3~1/RELEASE_X86_64 x86_64

echo $user | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo aneg

aneg

echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo setenv SUBJECTS_DIR /Users/aneg/analyses/EMOT_REG_RECON_DISS

setenv SUBJECTS_DIR /Users/aneg/analyses/EMOT_REG_RECON_DISS

echo "FREESURFER_HOME $FREESURFER_HOME" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo FREESURFER_HOME /Applications/freesurfer

FREESURFER_HOME /Applications/freesurfer

echo "" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo

echo "Original mri_glmfit command line:" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo Original mri_glmfit command line:

Original mri_glmfit command line:

echo $glmfitcmd0 | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo cmdline mri_glmfit --y GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz --wls GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz --osgm --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --nii.gz

cmdline mri_glmfit --y GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/ces.nii.gz --wls GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/cesvar.nii.gz --osgm --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ --nii.gz

echo "" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo

echo "DoSim = $DoSim" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoSim = 0

DoSim = 0

echo "UseCache = $UseCache" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo UseCache = 1

UseCache = 1

echo "DoPoll = $DoPoll" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoPoll = 0

DoPoll = 0

echo "DoPBSubmit = $DoPBSubmit" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoPBSubmit = 0

DoPBSubmit = 0

echo "DoBackground = $DoBackground" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DoBackground = 0

DoBackground = 0

echo "DiagCluster = $DiagCluster" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo DiagCluster = 0

DiagCluster = 0

echo "gd2mtx = $gd2mtx" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo gd2mtx = dods

gd2mtx = dods

if ( $#Seed ) echo "Seed = $Seed" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

if ( 0 ) echo Seed =

echo "fwhm = $fwhm" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo fwhm = 9.625207

fwhm = 9.625207

if ( $#fwhmOverride ) then

if ( 0 ) then

if ( $UseCache ) then

if ( 1 ) then

set fwhm = `cat $glmdir/fwhm.dat` ;

set fwhm = `cat $glmdir/fwhm.dat`

cat GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//fwhm.dat

set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+.5 ) ) "`

set fwhmStr = `perl -e "printf('"'%02d'"',int ( $fwhm+.5 ) ) "`

perl -e printf('%02d',int ( 9.625207+.5 ) )

set threshStr = `perl -e "print 10*$thresh"` ;

set threshStr = `perl -e "print 10*$thresh"`

perl -e print 10*1.3

set csdCache = $CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd

set csdCache = /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd

if ( ! -e $csdCache ) then

if ( ! -e /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd ) then

echo "ERROR: cannot find $csdCache" | tee -a $LF

tee -a GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls//cache.mri_glmfit-sim.log

echo ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd

ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd

exit 1 ;

exit 1

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Age (days ago)

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Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

3 comments

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tags (0)

participants (3)

Aly Negreira
Douglas Greve
Douglas N Greve