Hi Doug, The FSGD file is attached.
Best wishes,
Gill
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@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-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@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-boun...@nmr.mgh.harvard.edu
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
>> [gr...@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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>> gr...@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
>>
>>
>> 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
>> http://www.partners.org/complianceline . 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.
>>
>>
>> _______________________________________________
>> 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
> gr...@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
gr...@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
HRR60.fsgd
Description: HRR60.fsgd
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 http://www.partners.org/complianceline . 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.
