Hi Doug,
The FSGD file is attached.
Best wishes,
Gill
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Hmm, still not sure what's up. Can you attach your fsgd file to an email?
doug
On 11/05/2014 05:48 PM, Cooke, Gillian wrote:
Thanks Doug - this is what it produces:
out mris_preproc/lh.HRR60.thickness.10.mgh
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 10 != 0 )
set flag = $argv[1] ; shift ;
set flag = --fsgd
shift
switch ( $flag )
switch ( --fsgd )
if ( $#argv == 0 ) goto arg1err ;
if ( 9 == 0 ) goto arg1err
set fsgdf = $argv[1] ; shift ;
set fsgdf = fsgd/HRR60.fsgd
shift
if ( ! -e $fsgdf ) then
if ( ! -e fsgd/HRR60.fsgd ) then
set sl = `cat $fsgdf | awk '{if($1 == "Input") print $2}'` ;
set sl = `cat $fsgdf | awk '{if($1 == "Input") print $2}'`
cat fsgd/HRR60.fsgd
awk {if($1 == "Input") print $2}
set subjlist = ( $subjlist $sl ) ;
set subjlist = ( )
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 8 != 0 )
set flag = $argv[1] ; shift ;
set flag = --cache-in
shift
switch ( $flag )
switch ( --cache-in )
if ( $#argv < 1 ) goto arg1err ;
if ( 7 < 1 ) goto arg1err
set meas = $argv[1] ; shift ;
set meas = thickness.fwhm10.fsaverage
shift
set srcsurf = 1 ;
set srcsurf = 1
set CacheIn = 1 ;
set CacheIn = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 6 != 0 )
set flag = $argv[1] ; shift ;
set flag = --target
shift
switch ( $flag )
switch ( --target )
if ( $#argv == 0 ) goto arg1err ;
if ( 5 == 0 ) goto arg1err
set target = $argv[1] ; shift ;
set target = fsaverage
shift
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 4 != 0 )
set flag = $argv[1] ; shift ;
set flag = --hemi
shift
switch ( $flag )
switch ( --hemi )
if ( $#argv == 0 ) goto arg1err ;
if ( 3 == 0 ) goto arg1err
set srchemi = $argv[1] ; shift ;
set srchemi = lh
shift
set trghemi = $srchemi ;
set trghemi = lh
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --out
shift
switch ( $flag )
switch ( --out )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set outpath = $argv[1] ; shift ;
set outpath = mris_preproc/lh.HRR60.thickness.10.mgh
shift
set outstem = `fname2stem $outpath`
set outstem = `fname2stem $outpath`
fname2stem mris_preproc/lh.HRR60.thickness.10.mgh
if ( $status ) then
if ( 0 ) then
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 0 != 0 )
goto parse_args_return ;
goto parse_args_return
goto handle_fsfast ;
goto handle_fsfast
if ( $#SessFile ) then
if ( 0 ) then
goto handle_fsfast_return ;
goto handle_fsfast_return
goto check_params ;
goto check_params
if ( $#subjlistfile && $#ivplist ) then
if ( 0 && 0 ) then
if ( $#subjlistfile && $#fsgdf ) then
if ( 0 && 1 ) then
if ( $#ivplist && $#fsgdf ) then
if ( 0 && 1 ) then
if ( $#subjlist == 0 ) then
if ( 0 == 0 ) then
echo "ERROR: no subjects specified"
echo ERROR: no subjects specified
ERROR: no subjects specified
exit 1 ;
exit 1
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
run it like this
mris_preproc --debug --fsgd fsgd/HRR60.fsgd ...
doug
On 11/05/2014 05:32 PM, Cooke, Gillian wrote:
Unfortunately I'm getting this error in the terminal:
bash: --debug: command not found
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu]
Sent: Wednesday, November 05, 2014 4:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error
Can you run it with --debug as the first argument and send the terminal
output?
doug
On 11/05/2014 04:21 PM, Cooke, Gillian wrote:
Hi All,
I am getting a consistent error when I try to run mris_preproc - I'm
baffled as I've used all of my scripts and fsgd files before.
There are 2 groups with 3 covariates but I keep getting this error:
mris_preproc --fsgd fsgd/HRR60.fsgd --cache-in
thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out
mris_preproc/lh.HRR60.thickness.10.mgh
ERROR: no subjects specified
But my fsgd file lists all subject numbers:
GroupDescriptorFile 1
Title ACCE HRR60
Class Control
Class Cancer
VariablesAge_demeanedEd_demeanedHRR60
Input505_1Cancer-5.631.543
Input506_1Cancer7.373.553
Input509_1Cancer4.37-0.544
Input517_1Cancer-20.63-1.538
Input518_1Cancer-4.63-2.535
Input520_1Cancer0.371.537
Input521_1Control3.371.549
Input524_1Cancer3.37-0.532
Input525_1Control-12.63-2.551
#Input528_1Cancer10.373.5
Input529_1Control-28.634.532
Input530_1Cancer1.371.524
Input531_1Cancer6.377.555
Input532_1Cancer-1.631.514
Input533_1Cancer-10.633.536
Input534_1Control-3.631.525
Input536_1Control-11.63047
Input547_1Control10.371.525
Input548_1Control-18.63-0.546
Input549_1Cancer-21.63-0.538
Input554_1Control-21.63-0.538
Input558_1Cancer9.37-1.524
Input563_1Control0.370.530
Input564_1Control7.371.514
Any help is greatly appreciated!
Gill
_____________________
Gillian Cooke, Ph.D.
Postdoctoral Research Associate
Lifelong Brain & Cognition Lab
Decision Neuroscience Lab
Beckman Institute
University of Illinois, Urbana
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MGH-NMR Center
greve@nmr.mgh.harvard.edu
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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/
_______________________________________________
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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/
_______________________________________________
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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