Hi Doug,
this is the result it printed out in the terminal:
etsch:/scr/etsch2/kids$ mris_preproc --debug --qdec-long long.qdec.table.dat
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw
end
end
while ( $#argv != 0 )
while ( 2 != 0 )
set flag = $argv[1] ; shift ;
set flag = --qdec-long
shift
switch ( $flag )
switch ( --qdec-long )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set fsgdf = $argv[1] ; shift ;
set fsgdf = long.qdec.table.dat
shift
if ( ! -e $fsgdf ) then
if ( ! -e long.qdec.table.dat ) then
set sl = `cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#")
printf("%s.long.%s\n", $1, $2)}'` ;
set sl = `cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#")
printf("%s.long.%s\n", $1, $2)}'`
awk {if ($1 != "fsid" && substr($1,0,1) != "#") printf("%s.long.%s\n", $1, $2)}
cat long.qdec.table.dat
set subjlist = ( $subjlist $sl ) ;
set subjlist = ( AL3K_1.long.AL3K.base AL3K_2.long.AL3K.base
AL3K_3.long.AL3K.base AM1K_1.long.AM1K.base AM1K_2.long.AM1K.base
AM1K_3.long.AM1K.base BJ4K_1.long.BJ4K.base BJ4K_2.long.BJ4K.base
BJ4K_3.long.BJ4K.base BJ8K_1.long.BJ8K.base BJ8K_2.long.BJ8K.base
BJ8K_3.long.BJ8K.base BN2K_1.long.BN2K.base BN2K_2.long.BN2K.base
BN2K_3.long.BN2K.base WL3K_1.long.WL3K.base WL3K_2.long.WL3K.base
WL3K_3.long.WL3K.base ZF1K_1.long.ZF1K.base ZF1K_2.long.ZF1K.base
ZF1K_3.long.ZF1K.base .long. )
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 ( 22 == 0 ) then
if ( $#srchemi == 0 ) then
if ( 0 == 0 ) then
echo "ERROR: no source hemi specified"
echo ERROR: no source hemi specified
ERROR: no source hemi specified
exit 1 ;
exit 1
Cheers, Clara
----- Ursprüngliche Mail -----
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 13. August 2015 22:10:26
Betreff: Re: [Freesurfer] cannot find qdec file
I'm not sure what to tell you. When I use the new file I don't get an
error. When I use the old one I do. Can you run
mris_preproc --debug --qdec-long long.qdec.table.dat
and send me the result?
On 08/13/2015 01:01 PM, Clara Kühn wrote:
> do you mean the one without the blank line at the end? I've attached that for
> you.
> Cheers, Clara
>
> ----- Ursprüngliche Mail -----
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 13. August 2015 18:12:40
> Betreff: Re: [Freesurfer] cannot find qdec file
>
> Can you send the new qdec table file?
>
> On 08/05/2015 04:05 AM, Clara Kühn wrote:
>> no worries!
>> sadly, though, deleting the empty line wasn't the answer to the problem :(
>> Cheers, Clara
>>
>> ----- Ursprüngliche Mail -----
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Dienstag, 4. August 2015 20:43:47
>> Betreff: Re: [Freesurfer] cannot find qdec file
>>
>> oops, sorry for the delay, thanks for the reminder. The problem is that
>> you have a blank line at the end of your long.qdec.table.dat file.
>> Remove the line and see if it works.
>> doug
>>
>> On 08/04/2015 12:42 PM, Clara Kühn wrote:
>>> Hi Doug,
>>> did the fordoug.log file give any information about why FreeSurfer can't
>>> find my qdec file?
>>>
>>> Cheers and thanks for working on this!
>>> Clara
>>>
>>> ----- Ursprüngliche Mail -----
>>> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Montag, 3. August 2015 17:16:18
>>> Betreff: Re: [Freesurfer] cannot find qdec file
>>>
>>> can you run
>>>
>>> mris_preproc --debug --qdec-long
>>> /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1
>>> --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh
>>> |& tee fordoug.log
>>>
>>> and send me fordoug.log ?
>>>
>>>
>>> On 8/3/15 10:38 AM, Clara Kühn wrote:
>>>
>>>
>>>
>>> the command line is this:
>>> mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat
>>> --target 7kids_template_sc1 --hemi lh --meas thickness --out
>>> /scr/etsch2/kids/ct/qdec/lh.thickness.mgh
>>>
>>> the terminal output is this:
>>> nsubjects = 22
>>> ERROR: cannot find /scr/etsch2/kids/ct/.long.
>>>
>>> and the actual qdec file is attached.
>>> Cheers, Clara
>>>
>>> ----- Ursprüngliche Mail -----
>>> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> An:
>>> freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24
>>> Betreff: Re: [Freesurfer] cannot find qdec file
>>>
>>> Can you send your command line, full terminal output, and your
>>> long.qdec.table.dat file?
>>>
>>> On 8/3/15 10:31 AM, Clara Kühn wrote:
>>>
>>>
>>>
>>> ok, it can only access the file if I type
>>> ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash)
>>>
>>> but if I then use that path for the mris_preproc command I get
>>> nsubjects = 22
>>> ERROR: cannot find /scr/etsch2/kids/ct/.long.
>>>
>>>
>>>
>>> ----- Ursprüngliche Mail -----
>>> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> An:
>>> freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48
>>> Betreff: Re: [Freesurfer] cannot find qdec file
>>>
>>> that is probably not the full path. Try typing
>>>
>>> ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat
>>>
>>> If it says it cannot find the file, then it is not the full path. Maybe
>>> you need a forward slash (ie, "/") in the beginning?
>>>
>>> On 8/3/15 10:18 AM, Clara Kühn wrote:
>>>
>>>
>>>
>>> then I get the error ERROR: cannot find
>>> scr/etsch2/kids/ct/qdec/long.qdec.table.dat
>>>
>>> I had tried that. Sorry, no luck with that.
>>>
>>> ----- Ursprüngliche Mail -----
>>> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> An:
>>> freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58
>>> Betreff: Re: [Freesurfer] cannot find qdec file
>>>
>>> you have to give it the entire path to the file
>>>
>>> On 8/3/15 10:14 AM, Clara Kühn wrote:
>>>
>>>
>>>
>>> Dear FS-experts,
>>>
>>> I want to analyze my longitudinal data with your suggested LME models and
>>> am therefore following the walkthrough by J. Bernal. I get an error though
>>> very early on when using the command
>>> mris_preproc --qdec-long qdec/long.qdec.table.dat --target
>>> 7kids_template_sc1 --hemi lh --meas thickness --out qdec/lh.thickness.mgh
>>>
>>> It always says
>>> ERROR: cannot find qdec/long.qdec.table.dat
>>>
>>> Yes, the walkthrough asks for an input file named just qdec.table.dat, but
>>> I haven't got that. So far in the longitudinal stream there are
>>> long.qdec.table.dat and cross.qdec.table.dat files but no simple
>>> qdec.table.dat files. So I figured I'd use the long.qdec file because FS
>>> needs to get the information about the long timepoints.
>>> But it cannot find the file, even though I see it. I've also tried copying
>>> the long.qdec file and naming it qdec.table.dat but it still doesn't find
>>> it.
>>>
>>> The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat
>>> and my SUBJECTS_DIR is scr/etsch2/kids/ct
>>>
>>> Can you help me see what I'm missing?
>>> Thanks a lot in advance,
>>> Clara
>>> _______________________________________________
>>> 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 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.
>>>
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>>> _______________________________________________
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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
>>>
>>>
>>> _______________________________________________
>>> 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
>>>
>>>
>>> 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
>>>
>>>
>
>
> _______________________________________________
> 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
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