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Dear Sir or Madam,
I am currently trying to run a group analysis on FreeSurfer. After having created a FSGD-File I tried mris_prepoc. As a command I use
mris_preproc --fsgd FSGD_File_Aggression.fsgd --cache-in
thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out
lh.gender_age.thickness.10.mgh.
My FSGD-File looks like this.
GroupDesriptorFile 1
Title Aggression Martial Arts
Class 0
Class 1
Variables Age
Input zv75 0 27
Input xp09 0 26
Input wn791 24
Input wi40 0 19
Input vg03 0 33
Input va82 1 24
Input ui42 1 23
Input ud16 0 26
Input tp38 1 22
Input to98 1 22
Input th01 0 23
Input tg08 1 23
Input so80 1 21
Input re37 0 27
Input pt12 1 27
Input pl96 1 22
Input pi04 1 27
Input oo75 0 22
Input ob56 1 23
Input nh85 1 27
Input mw53 1 23
Input lu75 0 22
Input lt62 1 22
Input le00 0 23
Input lc79 1 24
Input kp89 0 22
Input ko71 1 25
Input ke93 0 29
Input ju55 0 20
Input jc49 0 21
Input in19 1 29
Input if27 0 29
Input hc55 1 23
Input gs02 0 43
Input fp50 1 21
Input ez57 1 25
Input et53 1 24
Input ei77 1 27
Input dn20 1 28
Input cp97 0 25
Input cn18 1 52
Input cm66 0 21
Input cg21 1 22
Input bw90 0 29
Input bg38 1 25
Input ab35 0 22
Title Aggression Martial Arts
Class 0
Class 1
Variables Age
Input zv75 0 27
Input xp09 0 26
Input wn791 24
Input wi40 0 19
Input vg03 0 33
Input va82 1 24
Input ui42 1 23
Input ud16 0 26
Input tp38 1 22
Input to98 1 22
Input th01 0 23
Input tg08 1 23
Input so80 1 21
Input re37 0 27
Input pt12 1 27
Input pl96 1 22
Input pi04 1 27
Input oo75 0 22
Input ob56 1 23
Input nh85 1 27
Input mw53 1 23
Input lu75 0 22
Input lt62 1 22
Input le00 0 23
Input lc79 1 24
Input kp89 0 22
Input ko71 1 25
Input ke93 0 29
Input ju55 0 20
Input jc49 0 21
Input in19 1 29
Input if27 0 29
Input hc55 1 23
Input gs02 0 43
Input fp50 1 21
Input ez57 1 25
Input et53 1 24
Input ei77 1 27
Input dn20 1 28
Input cp97 0 25
Input cn18 1 52
Input cm66 0 21
Input cg21 1 22
Input bw90 0 29
Input bg38 1 25
Input ab35 0 22
However FreeSurfer always metions that there are no subjects specified. So, this is what I tried today.
Last login: Mon Nov 5 14:12:34 on ttys000
kpsy-mac84024:~ Forschung$ ls
All_regions.jpg
CONN_autorecovery_project_07-Jun-2017-15-51-32
CONN_autorecovery_project_07-Jun-2017-15-51-32.mat
DTI
Desktop
Documents
Dokumente
Downloads
ENIGMA_QC
Library
Movies
Music
Pictures
Public
QC
TIV.txt
aparc_area_lh.txt
aparc_meancurv_lh.txt
aparc_thickness_lh.txt
aparc_thickness_rh.txt
aparc_volume_rh.txt
catlog_main_20180302_124731_log01.txt
error.log
export
m.mat
matlab
matlab_crash_dump.378-1
matlab_crash_dump.466-1
matlab_crash_dump.495-1
setenv
source
test3333.txt
kpsy-mac84024:~ Forschung$ pwd
/Users/Forschung
kpsy-mac84024:~ Forschung$ cd Dektop/
-bash: cd: Dektop/: No such file or directory
kpsy-mac84024:~ Forschung$ cd Desktop/
kpsy-mac84024:Desktop Forschung$ cd Larissa/
kpsy-mac84024:Larissa Forschung$ cd Gewalt/
kpsy-mac84024:Gewalt Forschung$ ls
Correlate 13.spv
FSGD_File_Aggression.fsgd
FSGD_File_Aggression.fsgtr´r´´n´FSGD_File_Aggression.txt
Lateroorbitofrontal r GruppeFAV.spv
Pars opercularis r Gruppe.spv
ab35
aparc_area_lh.txt
aparc_area_rh.txt
aparc_meancurv_lh.txt
aparc_meancurv_rh.txt
aparc_thickness_lh.txt
aparc_thickness_rh.txt
aparc_volume_rh.txt
aseg_stats.txt
bg38
bw90
caudatur r Gruppe.spv
cg21
cm66
cn18
cp97
ct23
dn20
ei77
error.log
et53
ez57
fp50
glm
gs02
hc55
if27
in19
jc49
ju55
ke93
ko71
kp89
lc79
le00
lh.BA.area.txt
lh.BA.meancurv.txt
lh.BA.thickness.txt
lh.BA.volume.txt
lh.a2009s.area.txt
lh.a2009s.meancurv.txt
lh.a2009s.thickness.txt
lh.a2009s.volume.txt
lt62
lu75
mw53
nh85
ob56
oo75
pi04
pl96
pt12
re37
rh.BA.area.txt
rh.BA.meancurv.txt
rh.BA.thickness.txt
rh.BA.volume.txt
rh.a2009s.area.txt
rh.a2009s.meancurv.txt
rh.a2009s.thickness.txt
rh.a2009s.volume.txt
so80
tg08
th01
to98
tp38
ud16
ui42
va82
vg03
wi40
wmparc_stats.txt
wn79
xp09
zv75
kpsy-mac84024:Gewalt Forschung$ mv FSGD_File_Aggression.fsgd
usage: mv [-f | -i | -n] [-v] source target
mv [-f | -i | -n] [-v] source ... directory
kpsy-mac84024:Gewalt Forschung$ mris_preproc --fsgd FSGD_File_Aggression.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
-bash: mris_preproc: command not found
kpsy-mac84024:Gewalt Forschung$ bash
bash-3.2$ csh
[kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% setenv
TERM_PROGRAM=Apple_Terminal
TERM=xterm-256color
SHELL=/bin/bash
TMPDIR=/var/folders/jy/b26gtv1s0tb7smwrvlc4233h0000gp/T/
Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.T97ejGsUvc/Render
TERM_PROGRAM_VERSION=361.1
TERM_SESSION_ID=B9E4C78C-6C45-419B-ABDF-33C85ADC9B42
USER=Forschung
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.wVr5HHnUoE/Listeners
__CF_USER_TEXT_ENCODING=0x1F6:0x0:0x3
PATH=/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
_=/bin/csh
PWD=/Users/Forschung/Desktop/Larissa/Gewalt
LANG=de_DE.UTF-8
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
HOME=/Users/Forschung
SHLVL=3
LOGNAME=Forschung
DISPLAY=/private/tmp/com.apple.launchd.Qt4G1Gdu4d/org.macosforge.xquartz:0
HOSTTYPE=unknown
VENDOR=apple
OSTYPE=darwin
MACHTYPE=x86_64
GROUP=staff
HOST=kpsy-mac84024.imed.uni-magdeburg.de
[kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% stenv
stenv: Command not found.
[kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% ls
Correlate 13.spv
FSGD_File_Aggression.fsgd
FSGD_File_Aggression.fsgtr´r´´n´FSGD_File_Aggression.txt
Lateroorbitofrontal r GruppeFAV.spv
Pars opercularis r Gruppe.spv
ab35
aparc_area_lh.txt
aparc_area_rh.txt
aparc_meancurv_lh.txt
aparc_meancurv_rh.txt
aparc_thickness_lh.txt
aparc_thickness_rh.txt
aparc_volume_rh.txt
aseg_stats.txt
bg38
bw90
caudatur r Gruppe.spv
cg21
cm66
cn18
cp97
ct23
dn20
ei77
error.log
et53
ez57
fp50
glm
gs02
hc55
if27
in19
jc49
ju55
ke93
ko71
kp89
lc79
le00
lh.BA.area.txt
lh.BA.meancurv.txt
lh.BA.thickness.txt
lh.BA.volume.txt
lh.a2009s.area.txt
lh.a2009s.meancurv.txt
lh.a2009s.thickness.txt
lh.a2009s.volume.txt
lt62
lu75
mw53
nh85
ob56
oo75
pi04
pl96
pt12
re37
rh.BA.area.txt
rh.BA.meancurv.txt
rh.BA.thickness.txt
rh.BA.volume.txt
rh.a2009s.area.txt
rh.a2009s.meancurv.txt
rh.a2009s.thickness.txt
rh.a2009s.volume.txt
so80
tg08
th01
to98
tp38
ud16
ui42
va82
vg03
wi40
wmparc_stats.txt
wn79
xp09
zv75
[kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% mris_preproc --fsgd FSGD_File_Aggression.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
mris_preproc: Command not found.
ERROR: no subjects specified[kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% ERROR: no subjects specified.
kpsy-mac84024:~ Forschung$ ls
All_regions.jpg
CONN_autorecovery_project_07-Jun-2017-15-51-32
CONN_autorecovery_project_07-Jun-2017-15-51-32.mat
DTI
Desktop
Documents
Dokumente
Downloads
ENIGMA_QC
Library
Movies
Music
Pictures
Public
QC
TIV.txt
aparc_area_lh.txt
aparc_meancurv_lh.txt
aparc_thickness_lh.txt
aparc_thickness_rh.txt
aparc_volume_rh.txt
catlog_main_20180302_124731_log01.txt
error.log
export
m.mat
matlab
matlab_crash_dump.378-1
matlab_crash_dump.466-1
matlab_crash_dump.495-1
setenv
source
test3333.txt
kpsy-mac84024:~ Forschung$ pwd
/Users/Forschung
kpsy-mac84024:~ Forschung$ cd Dektop/
-bash: cd: Dektop/: No such file or directory
kpsy-mac84024:~ Forschung$ cd Desktop/
kpsy-mac84024:Desktop Forschung$ cd Larissa/
kpsy-mac84024:Larissa Forschung$ cd Gewalt/
kpsy-mac84024:Gewalt Forschung$ ls
Correlate 13.spv
FSGD_File_Aggression.fsgd
FSGD_File_Aggression.fsgtr´r´´n´FSGD_File_Aggression.txt
Lateroorbitofrontal r GruppeFAV.spv
Pars opercularis r Gruppe.spv
ab35
aparc_area_lh.txt
aparc_area_rh.txt
aparc_meancurv_lh.txt
aparc_meancurv_rh.txt
aparc_thickness_lh.txt
aparc_thickness_rh.txt
aparc_volume_rh.txt
aseg_stats.txt
bg38
bw90
caudatur r Gruppe.spv
cg21
cm66
cn18
cp97
ct23
dn20
ei77
error.log
et53
ez57
fp50
glm
gs02
hc55
if27
in19
jc49
ju55
ke93
ko71
kp89
lc79
le00
lh.BA.area.txt
lh.BA.meancurv.txt
lh.BA.thickness.txt
lh.BA.volume.txt
lh.a2009s.area.txt
lh.a2009s.meancurv.txt
lh.a2009s.thickness.txt
lh.a2009s.volume.txt
lt62
lu75
mw53
nh85
ob56
oo75
pi04
pl96
pt12
re37
rh.BA.area.txt
rh.BA.meancurv.txt
rh.BA.thickness.txt
rh.BA.volume.txt
rh.a2009s.area.txt
rh.a2009s.meancurv.txt
rh.a2009s.thickness.txt
rh.a2009s.volume.txt
so80
tg08
th01
to98
tp38
ud16
ui42
va82
vg03
wi40
wmparc_stats.txt
wn79
xp09
zv75
kpsy-mac84024:Gewalt Forschung$ mv FSGD_File_Aggression.fsgd
usage: mv [-f | -i | -n] [-v] source target
mv [-f | -i | -n] [-v] source ... directory
kpsy-mac84024:Gewalt Forschung$ mris_preproc --fsgd FSGD_File_Aggression.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
-bash: mris_preproc: command not found
kpsy-mac84024:Gewalt Forschung$ bash
bash-3.2$ csh
[kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% setenv
TERM_PROGRAM=Apple_Terminal
TERM=xterm-256color
SHELL=/bin/bash
TMPDIR=/var/folders/jy/b26gtv1s0tb7smwrvlc4233h0000gp/T/
Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.T97ejGsUvc/Render
TERM_PROGRAM_VERSION=361.1
TERM_SESSION_ID=B9E4C78C-6C45-419B-ABDF-33C85ADC9B42
USER=Forschung
SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.wVr5HHnUoE/Listeners
__CF_USER_TEXT_ENCODING=0x1F6:0x0:0x3
PATH=/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
_=/bin/csh
PWD=/Users/Forschung/Desktop/Larissa/Gewalt
LANG=de_DE.UTF-8
XPC_FLAGS=0x0
XPC_SERVICE_NAME=0
HOME=/Users/Forschung
SHLVL=3
LOGNAME=Forschung
DISPLAY=/private/tmp/com.apple.launchd.Qt4G1Gdu4d/org.macosforge.xquartz:0
HOSTTYPE=unknown
VENDOR=apple
OSTYPE=darwin
MACHTYPE=x86_64
GROUP=staff
HOST=kpsy-mac84024.imed.uni-magdeburg.de
[kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% stenv
stenv: Command not found.
[kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% ls
Correlate 13.spv
FSGD_File_Aggression.fsgd
FSGD_File_Aggression.fsgtr´r´´n´FSGD_File_Aggression.txt
Lateroorbitofrontal r GruppeFAV.spv
Pars opercularis r Gruppe.spv
ab35
aparc_area_lh.txt
aparc_area_rh.txt
aparc_meancurv_lh.txt
aparc_meancurv_rh.txt
aparc_thickness_lh.txt
aparc_thickness_rh.txt
aparc_volume_rh.txt
aseg_stats.txt
bg38
bw90
caudatur r Gruppe.spv
cg21
cm66
cn18
cp97
ct23
dn20
ei77
error.log
et53
ez57
fp50
glm
gs02
hc55
if27
in19
jc49
ju55
ke93
ko71
kp89
lc79
le00
lh.BA.area.txt
lh.BA.meancurv.txt
lh.BA.thickness.txt
lh.BA.volume.txt
lh.a2009s.area.txt
lh.a2009s.meancurv.txt
lh.a2009s.thickness.txt
lh.a2009s.volume.txt
lt62
lu75
mw53
nh85
ob56
oo75
pi04
pl96
pt12
re37
rh.BA.area.txt
rh.BA.meancurv.txt
rh.BA.thickness.txt
rh.BA.volume.txt
rh.a2009s.area.txt
rh.a2009s.meancurv.txt
rh.a2009s.thickness.txt
rh.a2009s.volume.txt
so80
tg08
th01
to98
tp38
ud16
ui42
va82
vg03
wi40
wmparc_stats.txt
wn79
xp09
zv75
[kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% mris_preproc --fsgd FSGD_File_Aggression.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
mris_preproc: Command not found.
ERROR: no subjects specified[kpsy-mac84024:~/Desktop/Larissa/Gewalt] Forschung% ERROR: no subjects specified.
If you helped me with my problem I would be really grateful.
yours sincerely
Larissa Bechtle
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