Dear Doug,
Thanks for replying about fscalc. I read in the documentation that the two input files should typically be generated on the same subject. What I want to do is to add all the thickness .mgh files from my subjects together into one file. Is this possible with fscalc or another way? Right now I get an error about a size mismatch.
Thank you again!
Kind regards,
Rose ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of freesurfer-request@nmr.mgh.harvard.edu [freesurfer-request@nmr.mgh.harvard.edu] Sent: Thursday, July 13, 2017 12:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 23
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Today's Topics:
1. Re: UPDATE: Matlab Problem LME (Diers, Kersten /DZNE) 2. Re: mri_glmfit-sim ERROR cannot find mc-z.csd file (Douglas N Greve) 3. Re: Subject with missing fMRI data {Disarmed} (Douglas N Greve) 4. Re: Running segmentation on spatially normalized data (Douglas N Greve) 5. Re: asegstats2table error (Douglas N Greve) 6. Re: Strange Discrepancy Between Activation Location on Surface vs. Volume (Douglas N Greve) 7. Re: Qdec error in analysis (Douglas N Greve) 8. Re: petsurfer stats for multiple segmentations (Douglas N Greve) 9. Re: Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0 (Douglas N Greve) 10. Re: Subject with missing fMRI data {Disarmed} (Sadie Marvel) 11. Re: Pial surface editing (Michelle VanTieghem) 12. Differences in volume between mri_segstats and mris_anatomical_stats (Bruss, Joel E) 13. Re: dmri_pathstats error (Yuwen Hung) 14. Re: dmri_pathstats error (Yuwen Hung) 15. Re: Pial surface editing (Bruce Fischl) 16. Re: petsurfer stats for multiple segmentations (Lu Zhao) 17. Re: Subject with missing fMRI data {Disarmed} (Douglas N Greve) 18. Re: petsurfer stats for multiple segmentations (Douglas N Greve) 19. Re: Differences in volume between mri_segstats and mris_anatomical_stats (Douglas N Greve) 20. Re: mkbrainmask-sess: couldn't find register.dof6.lta (Douglas N Greve) 21. Re: Subject with missing fMRI data {Disarmed} (Sadie Marvel) 22. Re: How to edit Fsgdf4G2V about the group.effect.mtx (Douglas N Greve) 23. TAR fs files (Schumman Resonance) 24. Re: BBRegister + partial FoV fail (Douglas N Greve) 25. Re: GLM question (Douglas N Greve) 26. Re: Simple math with freesurfer surfaces (Douglas N Greve) 27. Re: TAR fs files (Douglas N Greve) 28. Re: smoothing data (Douglas N Greve) 29. Re: smoothing data (Matt Glasser) 30. Re: TAR fs files (Bruce Fischl) 31. Re: TAR fs files (Schumman Resonance) 32. Re: How to edit Fsgdf4G2V about the group.effect.mtx (haidong wang) 33. Re: How to edit Fsgdf4G2V about the group.effect.mtx (Douglas Greve) 34. Re: BBRegister + partial FoV fail (Paul Glad Mihai) 35. 3G1V.fsgd (stdp82@virgilio.it) 36. FS 6.0 (Del Re, Elisabetta) 37. Re: FS 6.0 (Bruce Fischl) 38. Re: [External] Re: Differences in volume between mri_segstats and mris_anatomical_stats (Bruss, Joel E) 39. Pediatric Atlas/Template (Jessica Reynolds) 40. Pediatric Atlas/Template (Jessica Reynolds) 41. Pediatric Atlas/Template (Jessica Reynolds) 42. GLM Analysis Number of vertices and Area (Aman Montazeri)
----------------------------------------------------------------------
Message: 1 Date: Wed, 12 Jul 2017 18:14:58 +0200 From: "Diers, Kersten /DZNE" Kersten.Diers@dzne.de Subject: Re: [Freesurfer] UPDATE: Matlab Problem LME To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 1327935B-0065-4A56-98A8-8AF8F4DED407@dzne.de Content-Type: text/plain; charset="us-ascii"
Hi Clara,
thanks for the additional information, this is helpful!
If you are calling the scripts with
[lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere, lhRe, lhTh0, lhcortex, 2, 95);
then 'lhcortex' will contain the analysis mask, i.e. indices for those vertices for which the analysis will be performed.
'lhcortex' should already be a subset of the vertices specified by 'lhsphere', i.e. excluding some portions of the medial wall.
If you have zero-valued columns in your data matrix, one thing worth trying is to remove the corresponding indices from 'lhcortex', i.e. further restrict the analysis mask. This should be done before the initial covariance estimation, i.e. prior to calling lme_mass_fit_init or lme_mass_fit_EMinit. In addition, it is of course worthwhile to investigate the cause of the zero-columns.
Best,
Kersten
------------------------------
Message: 2 Date: Wed, 12 Jul 2017 12:17:45 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file To: freesurfer@nmr.mgh.harvard.edu Message-ID: a1d5416e-5e09-d7ab-e2c1-10c802dbe8be@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8; format=flowed
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/
------------------------------
Message: 3 Date: Wed, 12 Jul 2017 12:19:17 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed} To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5f1ae473-c099-44f9-396d-cff4730d1883@nmr.mgh.harvard.edu Content-Type: text/plain; charset=UTF-8; format=flowed
it might not be possible to use the frame mask with wls. Does it work without it?
On 07/09/2017 04:46 PM, Sadie Marvel wrote:
So now that I am using --no-prune, I'm getting this error: group wrfx error: MRInormWeights: value less than or eq to 0. ?I found another thread in the mailing list about this error saying that there may be values in cesvar.nii that are =0, and that pruning normally masks out these values. But here, I am trying to use my own masks to do so. Is it possible now that my masks and my --y input have different sizes? If so, how can I solve this?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Friday, July 7, 2017 11:57 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
Add --no-prune
On 7/7/17 11:38 AM, Sadie Marvel wrote:
?When I use a script like this,
mri_glmfit --y ces.nii --wls cesvar.nii --osgm --frame-mask masks.nii --surface fsaverage rh --glmdir my-glm2.wls --nii.gz?
using the individual binary masks for all the subjects, the command seems to revert to using mask.nii, the single mask that was averaged over subjects. The output then just looks like it was using the single mask instead of being subject specific. Any idea why?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Thursday, July 6, 2017 12:58 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
yes
On 7/6/17 12:50 PM, Sadie Marvel wrote:
From using isxconcat-sess to concatenate all of my subjects together, the command creates binary masks called masks.nii and mask.nii, masks.nii being all of the binary masks for each subject. Is this what I would use with --frame-mask?
Thanks,
Sadie
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Wednesday, July 5, 2017 7:28 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Subject with missing fMRI data
We don't have any tools to do imputation. It is possible to have a subject specific mask with the --frame-mask option to mri_glmfit. The frame mask must be the same size as the input (--y) with 1s and 0s to indicate whether a given voxel for a given subject should be included in the model. I've not been happy with this method as it can create some strange results as different voxels will now have different DOFs.
On 6/29/17 8:49 AM, Sadie Marvel wrote:
Hi List,
I am currently doing a group analysis of 26 subjects, one of which has missing fMRI data where the signal cuts off through parts of the occipital and temporal lobes. I was wondering if freesurfer has any way of dealing with this, such as multiple imputation, or other methods of filling the missing data. Alternatively, is there a way to only use the portions of the brain that have data when doing mri_glmfit? Does freesurfer do this automatically?
Thanks.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be* 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
-- 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/
------------------------------
Message: 4 Date: Wed, 12 Jul 2017 12:23:53 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Running segmentation on spatially normalized data To: freesurfer@nmr.mgh.harvard.edu Message-ID: 9c6996a8-dbd2-8c58-4f06-ae7cc2c6ae8f@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed
sorry, I don't know anything about .tlrc files (or much about AFNI). If the transform is linear, then you should be able to map between the spaces with mri_vol2vol or mri_label2vol, but you will need to get the transform into a FS-compatible format.
On 07/06/2017 01:50 PM, Lauren Stephanie Hopkins wrote:
Hi all:
We ran FreeSurfer's recon sequence of anatomy files that had already been aligned to the MNI template - so spatially normalized. We're doing all of our processing in AFNI and the resulting segmentation output files open in AFNI's orig space, not in tlrc space. So basically we can't overlay the segmentation files on our anat+tlrc files where they should already be aligned to each other. When we converted the file to a .tlrc file with the AFNI command 3dcopy we could then overlay the mask on the normalized anatomy but it was no longer aligned.
So I suppose my question is - is there any way to have the segmentation files maintain their positioning or output in .tlrc space so they are still aligned to our anatomy files?
Thanks for any insight.
Lauren
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/
------------------------------
Message: 5 Date: Wed, 12 Jul 2017 12:27:20 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] asegstats2table error To: freesurfer@nmr.mgh.harvard.edu Message-ID: 614c9872-917a-9eb3-748e-12c1247ec242@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8; format=flowed
Not sure what the problem is, but it might be something specific to your site (looks like it cannot find the proper libraries to import). Can you run it at all. Eg, if just run the script without any arguments, do you get the same thing? What about if you run it with -h ?
On 07/06/2017 03:33 AM, Elizabeth Dao wrote:
Dear experts,
I have completed recon-all with no errors. Now I would like to use the 'asegstats2table' command but I've received the error below. I would appreciate any help in solving this problem. I am using FreeSurfer v6.0.0 on a Linux CentOS machine.
[TLA@CogmobCentOS MCI]$ asegstats2table --subjects 201.MR1 202.MR1 203.MR1 --meas volume --tablefile aseg_stats_all.txt 'import site' failed; use -v for traceback Traceback (most recent call last): File "/home/TLA/Desktop/Liz/freesurfer6/bin/asegstats2table", line 4, in <module> import os File "/usr/local/lib/python2.7/os.py", line 398, in <module> import UserDict File "/usr/local/lib/python2.7/UserDict.py", line 84, in <module> _abcoll.MutableMapping.register(IterableUserDict) File "/usr/local/lib/python2.7/abc.py", line 109, in register if issubclass(subclass, cls): File "/usr/local/lib/python2.7/abc.py", line 184, in __subclasscheck__ cls._abc_negative_cache.add(subclass) File "/usr/local/lib/python2.7/_weakrefset.py", line 84, in add self.data.add(ref(item, self._remove)) TypeError: cannot create weak reference to 'classobj' object
Thank you in advance for your help!
Liz
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/
------------------------------
Message: 6 Date: Wed, 12 Jul 2017 12:32:02 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Strange Discrepancy Between Activation Location on Surface vs. Volume To: freesurfer@nmr.mgh.harvard.edu Message-ID: 7e0e01ff-08b1-636d-bdf7-aec2586ea290@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8; format=flowed
Hi Johnmark, sorry, I can't reconstruct the thread from the earlier emails. Can you resubmit with just the thread from your email and not all 29 threads from July 5?
thanks
doug
On 07/06/2017 02:00 PM, Taylor, Johnmark wrote:
The subject name when I call tksurfer, the subject name when I call tkmedit, and the subject name in the registration file are all exactly the same: red_badger. One thing I noticed is that in the left hemisphere everything seems normal (the activation is in the expected location); things only look weird in the right hemisphere. There's no possibility that the surface reconstruction could have been off the mark? Though it seems implausible that it would take the IPS and somehow warp it all the way onto the medial surface of the brain...
Here are pictures of both the volume and surface views of the activation in question (it's the medial patch on the surface view, the patch with the red cursor in the volume view), in case they didn't load before for some reason.
????https://ibb.co/b8HFCv https://ibb.co/cWYcQF
On Thu, Jul 6, 2017 at 12:00 PM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu <mailto:freesurfer-owner@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: error message while using autorecon1 (Hoopes, Andrew) 2. Re: error message while using autorecon1 (Buckless, Colleen) 3. Re: Additional surface area (Bruce Fischl) 4. Fwd: remove skull from gtmseg.mgz (miracle ozzoude) 5. Re: error message while using autorecon1 (Hoopes, Andrew) 6. Re: error message while using autorecon1 (Buckless, Colleen) 7. Re: error message while using autorecon1 (Hoopes, Andrew) 8. Re: recon-all on newborn (Lilla Zollei) 9. Re: recon-all on newborn (Das S.) 10. Re: Still confused by group analysis.. (Douglas Greve) 11. Re: Raw Cortical thickness values (Douglas Greve) 12. Re: Average myelination within ROI (Douglas Greve) 13. Re: bbregister vs spmregister vs mri_coreg (Douglas Greve) 14. Re: Recon-all: too many ('s (Douglas Greve) 15. Re: Using multimodal slab input for hippocampus subfield segmentation in FS6 (Douglas Greve) 16. Re: Strange Discrepancy Between Activation Location on Surface vs. Volume (Douglas Greve) 17. Re: negative header after preproc-sess (Douglas Greve) 18. Re: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> (Douglas Greve) 19. Re: Building your own fsaverage (Douglas Greve) 20. Re: Qdec error in analysis (Douglas Greve) 21. Re: mri_glmfit error (mri_reshape number of elements) (Douglas Greve) 22. Re: Fwd: remove skull from gtmseg.mgz (Douglas Greve) 23. Re: GLM fitting for the cortical volume (Douglas Greve) 24. Re: Subject with missing fMRI data (Douglas Greve) 25. Re: Question mri_glmfit fwhm smoothing (Douglas Greve) 26. Re: viewing mri_glmfit FDR corrected results (Douglas Greve) 27. Re: content of "subjects_dir" (Douglas Greve) 28. Re: Qdec error in analysis (AYUSHI SHUKLA) 29. asegstats2table error (Elizabeth Dao) 30. Re: Fwd: remove skull from gtmseg.mgz (miracooloz@gmail.com <mailto:miracooloz@gmail.com>) ---------------------------------------------------------------------- Message: 1 Date: Wed, 5 Jul 2017 17:29:23 +0000 From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu <mailto:AHOOPES@mgh.harvard.edu>> Subject: Re: [Freesurfer] error message while using autorecon1 To: "'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>'" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <BLUPR04MB4662F945780124666F30CD2F9D40@BLUPR04MB466.namprd04.prod.outlook.com <mailto:BLUPR04MB4662F945780124666F30CD2F9D40@BLUPR04MB466.namprd04.prod.outlook.com>> Content-Type: text/plain; charset="Windows-1252" Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org>> Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>' Subject: [Freesurfer] error message while using autorecon1 Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all ?autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 <tel:443-923-2747> Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org> ________________________________ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ------------------------------ Message: 2 Date: Wed, 5 Jul 2017 17:36:47 +0000 From: "Buckless, Colleen" <Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org>> Subject: Re: [Freesurfer] error message while using autorecon1 To: "'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>'" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <6F20C54B58C269489AA5CC858A1F58AF95125F@GSP-MAIL1.kki.org <mailto:6F20C54B58C269489AA5CC858A1F58AF95125F@GSP-MAIL1.kki.org>> Content-Type: text/plain; charset="us-ascii" Hi Andrew, The output list includes nu_correct. Thanks, Colleen -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 1:29 PM To: 'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>' Subject: Re: [Freesurfer] error message while using autorecon1 Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org>> Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>' Subject: [Freesurfer] error message while using autorecon1 Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 <tel:443-923-2747> Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org> ________________________________ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=UD2JCpQKfeuIMEp7GIFvqrqCmqKkKCIa1NWotZOyhaY&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=UD2JCpQKfeuIMEp7GIFvqrqCmqKkKCIa1NWotZOyhaY&e=> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=fR9oEUmOUXaB4tibDHTZGg8YDMN_dAbvmLdoCVGkmaU&e= <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline&d=DwIF-g&c=-6Xp7zzYCOuh1vlHYMPGlLDGrbTByhvtrs9nrrENlxA&r=KT2lfyYGLO8_41MMS1kJM5RzqWQiVX82dUguebZ3MrY&m=U5y_JLvNNpCGs3DqsYe6vS_uCGTeasVXGNIwP3iBXIg&s=fR9oEUmOUXaB4tibDHTZGg8YDMN_dAbvmLdoCVGkmaU&e=> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ------------------------------ Message: 3 Date: Wed, 5 Jul 2017 13:51:41 -0400 (EDT) From: Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Additional surface area To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.20.1707051351070.31440@gate.nmr.mgh.harvard.edu <mailto:alpine.LRH.2.20.1707051351070.31440@gate.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Michael you need to look in the volume to see what is causing it. I would guess some dura that is being incorrectly included, but you will be able to tell in the slice view cheers Bruce On Mon, 3 Jul 2017, Michael Davies wrote: > > Hello, when inspecting a subject i discovered an anomaly on top of the 3D > surface i have not previously encountered on other subjects i have > inspected. Could you please let me know if this would be problematic when at > the analysing group data please? > > > Kind regards, Michael > > > ------------------------------ Message: 4 Date: Wed, 5 Jul 2017 13:53:57 -0400 From: miracle ozzoude <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> Subject: [Freesurfer] Fwd: remove skull from gtmseg.mgz To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <CANfOk0h=UyBU_4ZV0E9mEaoE0NMvvx1_A-x63JxaLxj=54nuLg@mail.gmail.com <mailto:54nuLg@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" ---------- Forwarded message ---------- From: miracle ozzoude <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> Date: Tue, Jul 4, 2017 at 10:23 AM Subject: remove skull from gtmseg.mgz To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Hello Freesurfer, After running the first step of PETsurfer (https://surfer.nmr.mgh. harvard.edu/fswiki/PetSurfer <http://harvard.edu/fswiki/PetSurfer>). I viewed the image it created using freeview. When I change, the color map to Lookup Table, the image also included the skull. How can I remove the skull from gtmseg.mgz/prevent it from showing? Any help will be appreciated. Thanks. Please, see attached image Best, Paul
Use mris_preproc to generate a stack of thicknesses in fsaverage space, then
mri_concat stack.mgh --mean --o stack.mean.mgh
On 07/13/2017 01:47 PM, Van Der Deijl, Rosanne wrote:
Dear Doug,
Thanks for replying about fscalc. I read in the documentation that the two input files should typically be generated on the same subject. What I want to do is to add all the thickness .mgh files from my subjects together into one file. Is this possible with fscalc or another way? Right now I get an error about a size mismatch.
Thank you again!
Kind regards,
Rose ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of freesurfer-request@nmr.mgh.harvard.edu [freesurfer-request@nmr.mgh.harvard.edu] Sent: Thursday, July 13, 2017 12:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 23
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
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Today's Topics:
1. Re: UPDATE: Matlab Problem LME (Diers, Kersten /DZNE) 2. Re: mri_glmfit-sim ERROR cannot find mc-z.csd file (Douglas N Greve) 3. Re: Subject with missing fMRI data {Disarmed} (Douglas N Greve) 4. Re: Running segmentation on spatially normalized data (Douglas N Greve) 5. Re: asegstats2table error (Douglas N Greve) 6. Re: Strange Discrepancy Between Activation Location on Surface vs. Volume (Douglas N Greve) 7. Re: Qdec error in analysis (Douglas N Greve) 8. Re: petsurfer stats for multiple segmentations (Douglas N Greve) 9. Re: Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0 (Douglas N Greve)
- Re: Subject with missing fMRI data {Disarmed} (Sadie Marvel)
- Re: Pial surface editing (Michelle VanTieghem)
- Differences in volume between mri_segstats and mris_anatomical_stats (Bruss, Joel E)
- Re: dmri_pathstats error (Yuwen Hung)
- Re: dmri_pathstats error (Yuwen Hung)
- Re: Pial surface editing (Bruce Fischl)
- Re: petsurfer stats for multiple segmentations (Lu Zhao)
- Re: Subject with missing fMRI data {Disarmed} (Douglas N Greve)
- Re: petsurfer stats for multiple segmentations (Douglas N Greve)
- Re: Differences in volume between mri_segstats and mris_anatomical_stats (Douglas N Greve)
- Re: mkbrainmask-sess: couldn't find register.dof6.lta (Douglas N Greve)
- Re: Subject with missing fMRI data {Disarmed} (Sadie Marvel)
- Re: How to edit Fsgdf4G2V about the group.effect.mtx (Douglas N Greve)
- TAR fs files (Schumman Resonance)
- Re: BBRegister + partial FoV fail (Douglas N Greve)
- Re: GLM question (Douglas N Greve)
- Re: Simple math with freesurfer surfaces (Douglas N Greve)
- Re: TAR fs files (Douglas N Greve)
- Re: smoothing data (Douglas N Greve)
- Re: smoothing data (Matt Glasser)
- Re: TAR fs files (Bruce Fischl)
- Re: TAR fs files (Schumman Resonance)
- Re: How to edit Fsgdf4G2V about the group.effect.mtx (haidong wang)
- Re: How to edit Fsgdf4G2V about the group.effect.mtx (Douglas Greve)
- Re: BBRegister + partial FoV fail (Paul Glad Mihai)
- 3G1V.fsgd (stdp82@virgilio.it)
- FS 6.0 (Del Re, Elisabetta)
- Re: FS 6.0 (Bruce Fischl)
- Re: [External] Re: Differences in volume between mri_segstats and mris_anatomical_stats (Bruss, Joel E)
- Pediatric Atlas/Template (Jessica Reynolds)
- Pediatric Atlas/Template (Jessica Reynolds)
- Pediatric Atlas/Template (Jessica Reynolds)
- GLM Analysis Number of vertices and Area (Aman Montazeri)
Message: 1 Date: Wed, 12 Jul 2017 18:14:58 +0200 From: "Diers, Kersten /DZNE" Kersten.Diers@dzne.de Subject: Re: [Freesurfer] UPDATE: Matlab Problem LME To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 1327935B-0065-4A56-98A8-8AF8F4DED407@dzne.de Content-Type: text/plain; charset="us-ascii"
Hi Clara,
thanks for the additional information, this is helpful!
If you are calling the scripts with
[lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere, lhRe, lhTh0, lhcortex, 2, 95);
then 'lhcortex' will contain the analysis mask, i.e. indices for those vertices for which the analysis will be performed.
'lhcortex' should already be a subset of the vertices specified by 'lhsphere', i.e. excluding some portions of the medial wall.
If you have zero-valued columns in your data matrix, one thing worth trying is to remove the corresponding indices from 'lhcortex', i.e. further restrict the analysis mask. This should be done before the initial covariance estimation, i.e. prior to calling lme_mass_fit_init or lme_mass_fit_EMinit. In addition, it is of course worthwhile to investigate the cause of the zero-columns.
Best,
Kersten
Message: 2 Date: Wed, 12 Jul 2017 12:17:45 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file To: freesurfer@nmr.mgh.harvard.edu Message-ID: a1d5416e-5e09-d7ab-e2c1-10c802dbe8be@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8; format=flowed
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
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-- 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/
Message: 3 Date: Wed, 12 Jul 2017 12:19:17 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Subject with missing fMRI data {Disarmed} To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5f1ae473-c099-44f9-396d-cff4730d1883@nmr.mgh.harvard.edu Content-Type: text/plain; charset=UTF-8; format=flowed
it might not be possible to use the frame mask with wls. Does it work without it?
On 07/09/2017 04:46 PM, Sadie Marvel wrote:
So now that I am using --no-prune, I'm getting this error: group wrfx error: MRInormWeights: value less than or eq to 0. ?I found another thread in the mailing list about this error saying that there may be values in cesvar.nii that are =0, and that pruning normally masks out these values. But here, I am trying to use my own masks to do so. Is it possible now that my masks and my --y input have different sizes? If so, how can I solve this?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Friday, July 7, 2017 11:57 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
Add --no-prune
On 7/7/17 11:38 AM, Sadie Marvel wrote:
?When I use a script like this,
mri_glmfit --y ces.nii --wls cesvar.nii --osgm --frame-mask masks.nii --surface fsaverage rh --glmdir my-glm2.wls --nii.gz?
using the individual binary masks for all the subjects, the command seems to revert to using mask.nii, the single mask that was averaged over subjects. The output then just looks like it was using the single mask instead of being subject specific. Any idea why?
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Thursday, July 6, 2017 12:58 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Subject with missing fMRI data {Disarmed}
yes
On 7/6/17 12:50 PM, Sadie Marvel wrote:
From using isxconcat-sess to concatenate all of my subjects together, the command creates binary masks called masks.nii and mask.nii, masks.nii being all of the binary masks for each subject. Is this what I would use with --frame-mask?
Thanks,
Sadie
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve greve@nmr.mgh.harvard.edu *Sent:* Wednesday, July 5, 2017 7:28 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Subject with missing fMRI data
We don't have any tools to do imputation. It is possible to have a subject specific mask with the --frame-mask option to mri_glmfit. The frame mask must be the same size as the input (--y) with 1s and 0s to indicate whether a given voxel for a given subject should be included in the model. I've not been happy with this method as it can create some strange results as different voxels will now have different DOFs.
On 6/29/17 8:49 AM, Sadie Marvel wrote:
Hi List,
I am currently doing a group analysis of 26 subjects, one of which has missing fMRI data where the signal cuts off through parts of the occipital and temporal lobes. I was wondering if freesurfer has any way of dealing with this, such as multiple imputation, or other methods of filling the missing data. Alternatively, is there a way to only use the portions of the brain that have data when doing mri_glmfit? Does freesurfer do this automatically?
Thanks.
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-- 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/
Message: 4 Date: Wed, 12 Jul 2017 12:23:53 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Running segmentation on spatially normalized data To: freesurfer@nmr.mgh.harvard.edu Message-ID: 9c6996a8-dbd2-8c58-4f06-ae7cc2c6ae8f@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed
sorry, I don't know anything about .tlrc files (or much about AFNI). If the transform is linear, then you should be able to map between the spaces with mri_vol2vol or mri_label2vol, but you will need to get the transform into a FS-compatible format.
On 07/06/2017 01:50 PM, Lauren Stephanie Hopkins wrote:
Hi all:
We ran FreeSurfer's recon sequence of anatomy files that had already been aligned to the MNI template - so spatially normalized. We're doing all of our processing in AFNI and the resulting segmentation output files open in AFNI's orig space, not in tlrc space. So basically we can't overlay the segmentation files on our anat+tlrc files where they should already be aligned to each other. When we converted the file to a .tlrc file with the AFNI command 3dcopy we could then overlay the mask on the normalized anatomy but it was no longer aligned.
So I suppose my question is - is there any way to have the segmentation files maintain their positioning or output in .tlrc space so they are still aligned to our anatomy files?
Thanks for any insight.
Lauren
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/
Message: 5 Date: Wed, 12 Jul 2017 12:27:20 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] asegstats2table error To: freesurfer@nmr.mgh.harvard.edu Message-ID: 614c9872-917a-9eb3-748e-12c1247ec242@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8; format=flowed
Not sure what the problem is, but it might be something specific to your site (looks like it cannot find the proper libraries to import). Can you run it at all. Eg, if just run the script without any arguments, do you get the same thing? What about if you run it with -h ?
On 07/06/2017 03:33 AM, Elizabeth Dao wrote:
Dear experts,
I have completed recon-all with no errors. Now I would like to use the 'asegstats2table' command but I've received the error below. I would appreciate any help in solving this problem. I am using FreeSurfer v6.0.0 on a Linux CentOS machine.
[TLA@CogmobCentOS MCI]$ asegstats2table --subjects 201.MR1 202.MR1 203.MR1 --meas volume --tablefile aseg_stats_all.txt 'import site' failed; use -v for traceback Traceback (most recent call last): File "/home/TLA/Desktop/Liz/freesurfer6/bin/asegstats2table", line 4, in <module> import os File "/usr/local/lib/python2.7/os.py", line 398, in <module> import UserDict File "/usr/local/lib/python2.7/UserDict.py", line 84, in <module> _abcoll.MutableMapping.register(IterableUserDict) File "/usr/local/lib/python2.7/abc.py", line 109, in register if issubclass(subclass, cls): File "/usr/local/lib/python2.7/abc.py", line 184, in __subclasscheck__ cls._abc_negative_cache.add(subclass) File "/usr/local/lib/python2.7/_weakrefset.py", line 84, in add self.data.add(ref(item, self._remove)) TypeError: cannot create weak reference to 'classobj' object
Thank you in advance for your help!
Liz
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-- 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/
Message: 6 Date: Wed, 12 Jul 2017 12:32:02 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Strange Discrepancy Between Activation Location on Surface vs. Volume To: freesurfer@nmr.mgh.harvard.edu Message-ID: 7e0e01ff-08b1-636d-bdf7-aec2586ea290@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8; format=flowed
Hi Johnmark, sorry, I can't reconstruct the thread from the earlier emails. Can you resubmit with just the thread from your email and not all 29 threads from July 5?
thanks
doug
On 07/06/2017 02:00 PM, Taylor, Johnmark wrote:
The subject name when I call tksurfer, the subject name when I call tkmedit, and the subject name in the registration file are all exactly the same: red_badger. One thing I noticed is that in the left hemisphere everything seems normal (the activation is in the expected location); things only look weird in the right hemisphere. There's no possibility that the surface reconstruction could have been off the mark? Though it seems implausible that it would take the IPS and somehow warp it all the way onto the medial surface of the brain...
Here are pictures of both the volume and surface views of the activation in question (it's the medial patch on the surface view, the patch with the red cursor in the volume view), in case they didn't load before for some reason.
????https://ibb.co/b8HFCv https://ibb.co/cWYcQF
On Thu, Jul 6, 2017 at 12:00 PM, <freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu <mailto:freesurfer-request@nmr.mgh.harvard.edu> You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu <mailto:freesurfer-owner@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: error message while using autorecon1 (Hoopes, Andrew) 2. Re: error message while using autorecon1 (Buckless, Colleen) 3. Re: Additional surface area (Bruce Fischl) 4. Fwd: remove skull from gtmseg.mgz (miracle ozzoude) 5. Re: error message while using autorecon1 (Hoopes, Andrew) 6. Re: error message while using autorecon1 (Buckless, Colleen) 7. Re: error message while using autorecon1 (Hoopes, Andrew) 8. Re: recon-all on newborn (Lilla Zollei) 9. Re: recon-all on newborn (Das S.) 10. Re: Still confused by group analysis.. (Douglas Greve) 11. Re: Raw Cortical thickness values (Douglas Greve) 12. Re: Average myelination within ROI (Douglas Greve) 13. Re: bbregister vs spmregister vs mri_coreg (Douglas Greve) 14. Re: Recon-all: too many ('s (Douglas Greve) 15. Re: Using multimodal slab input for hippocampus subfield segmentation in FS6 (Douglas Greve) 16. Re: Strange Discrepancy Between Activation Location on Surface vs. Volume (Douglas Greve) 17. Re: negative header after preproc-sess (Douglas Greve) 18. Re: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> (Douglas Greve) 19. Re: Building your own fsaverage (Douglas Greve) 20. Re: Qdec error in analysis (Douglas Greve) 21. Re: mri_glmfit error (mri_reshape number of elements) (Douglas Greve) 22. Re: Fwd: remove skull from gtmseg.mgz (Douglas Greve) 23. Re: GLM fitting for the cortical volume (Douglas Greve) 24. Re: Subject with missing fMRI data (Douglas Greve) 25. Re: Question mri_glmfit fwhm smoothing (Douglas Greve) 26. Re: viewing mri_glmfit FDR corrected results (Douglas Greve) 27. Re: content of "subjects_dir" (Douglas Greve) 28. Re: Qdec error in analysis (AYUSHI SHUKLA) 29. asegstats2table error (Elizabeth Dao) 30. Re: Fwd: remove skull from gtmseg.mgz (miracooloz@gmail.com <mailto:miracooloz@gmail.com>) ---------------------------------------------------------------------- Message: 1 Date: Wed, 5 Jul 2017 17:29:23 +0000 From: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu <mailto:AHOOPES@mgh.harvard.edu>> Subject: Re: [Freesurfer] error message while using autorecon1 To: "'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>'" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <BLUPR04MB4662F945780124666F30CD2F9D40@BLUPR04MB466.namprd04.prod.outlook.com <mailto:BLUPR04MB4662F945780124666F30CD2F9D40@BLUPR04MB466.namprd04.prod.outlook.com>> Content-Type: text/plain; charset="Windows-1252" Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org>> Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>' Subject: [Freesurfer] error message while using autorecon1 Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all ?autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 <tel:443-923-2747> Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org> ________________________________ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. ------------------------------ Message: 2 Date: Wed, 5 Jul 2017 17:36:47 +0000 From: "Buckless, Colleen" <Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org>> Subject: Re: [Freesurfer] error message while using autorecon1 To: "'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>'" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <6F20C54B58C269489AA5CC858A1F58AF95125F@GSP-MAIL1.kki.org <mailto:6F20C54B58C269489AA5CC858A1F58AF95125F@GSP-MAIL1.kki.org>> Content-Type: text/plain; charset="us-ascii" Hi Andrew, The output list includes nu_correct. Thanks, Colleen -----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 1:29 PM To: 'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>' Subject: Re: [Freesurfer] error message while using autorecon1 Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn't sourced. Andrew ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Buckless, Colleen <Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org>> Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>' Subject: [Freesurfer] error message while using autorecon1 Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 <tel:443-923-2747> Buckless@kennedykrieger.org <mailto:Buckless@kennedykrieger.org> ________________________________ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. 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If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ------------------------------ Message: 3 Date: Wed, 5 Jul 2017 13:51:41 -0400 (EDT) From: Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Additional surface area To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.20.1707051351070.31440@gate.nmr.mgh.harvard.edu <mailto:alpine.LRH.2.20.1707051351070.31440@gate.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset=US-ASCII; format=flowed Hi Michael you need to look in the volume to see what is causing it. I would guess some dura that is being incorrectly included, but you will be able to tell in the slice view cheers Bruce On Mon, 3 Jul 2017, Michael Davies wrote: > > Hello, when inspecting a subject i discovered an anomaly on top of the 3D > surface i have not previously encountered on other subjects i have > inspected. Could you please let me know if this would be problematic when at > the analysing group data please? > > > Kind regards, Michael > > > ------------------------------ Message: 4 Date: Wed, 5 Jul 2017 13:53:57 -0400 From: miracle ozzoude <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> Subject: [Freesurfer] Fwd: remove skull from gtmseg.mgz To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <CANfOk0h=UyBU_4ZV0E9mEaoE0NMvvx1_A-x63JxaLxj=54nuLg@mail.gmail.com <mailto:54nuLg@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" ---------- Forwarded message ---------- From: miracle ozzoude <miracooloz@gmail.com <mailto:miracooloz@gmail.com>> Date: Tue, Jul 4, 2017 at 10:23 AM Subject: remove skull from gtmseg.mgz To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Hello Freesurfer, After running the first step of PETsurfer (https://surfer.nmr.mgh. harvard.edu/fswiki/PetSurfer <http://harvard.edu/fswiki/PetSurfer>). I viewed the image it created using freeview. When I change, the color map to Lookup Table, the image also included the skull. How can I remove the skull from gtmseg.mgz/prevent it from showing? Any help will be appreciated. Thanks. Please, see attached image Best, Paul
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Van Der Deijl, Rosanne