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