18 Feb
2011
18 Feb
'11
5:32 p.m.
When I run this in version 4, it runs fine. Can you send me the full terminal output?
Pablo Polosecki wrote:
Hi Doug,
Sure, here is the command line with all the variables replaced by their actual values.
mkanalysis-sess \ -fsd bold \ -funcstem fmcus2 \ -analysis a1u \ -paradigm face_localizer_monkey.para \ -dt blocked \ -sf sf \ -df df \ -force \ -inorm \ -timewindow 40 \ -polyfit 2 \ -TR 2.0000 \ -gammafit 0 1.25 \ -gammaexp 2 \ -nconditions 7 \ -runlistfile rlf1 \ -mask brain_fmcu \ -taumax 20 \ -acfbins 1 \ -fix-acf \ -noautostimdur \ -motioncor -mcextreg
Thanks again,
Pablo
On Fri, Feb 18, 2011 at 12:33 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Can you send the actual command without any variables? thanks doug Pablo Polosecki wrote: Hi, The command line it's within the attached script, so it might not look as informative whn looked at on its own. However it is: mkanalysis-sess \ -fsd bold \ -funcstem $funcstem \ -analysis $analysis \ -paradigm $paradigm \ -dt blocked \ -sf sf \ -df df \ -force $tpef_string \ -inorm \ -timewindow ${timewindow} \ -polyfit 2 \ -TR $TR ${TER_string}\ -gammafit $gammafit \ -gammaexp $gammaexp \ -nconditions $nconditions \ -runlistfile $runlistfile \ -mask ${mask_stem} \ -taumax $taumax \ -acfbins 1 \ -fix-acf \ -noautostimdur \ -motioncor -mcextreg On Fri, Feb 18, 2011 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: What is your command-line? Pablo Polosecki wrote: Hi, I forgot to put the version, my bad. The version is 4.5. Thanks, Pablo On Fri, Feb 18, 2011 at 11:21 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: which version are you using? The seq.info <http://seq.info> <http://seq.info> <http://seq.info> file has not been used in a long time. doug Pablo Polosecki wrote: Hi all, I am trying to define an analysis for a block-based functional scan using mkanalysis-sess. When I run it, I get the following output with an error message: Setting TER to .10000000000000000000 /home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy ERROR: bad format for seq.info <http://seq.info> <http://seq.info> <http://seq.info> <http://seq.info> file, /home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy The seq.info <http://seq.info> <http://seq.info> <http://seq.info> <http://seq.info> file (attached) was produced by the unpacksdcmdir command and it looks no different from other ones I have seen. The information there seems correct to me. Could someone perhaps point out possible reasons why this could happen? The script I use to call mkanalysis-sess containing all the parameters used is attached. Thank you in advance. Pablo -- Pablo Polosecki Graduate Fellow Laboratory of Neural Systems The Rockefeller University 1230 York Avenue, Box 9 New York, NY 10065 Tel: 212-327-7699 (Lab) 917-842-2510 (Cell) email: ppolosecki@mail.rockefeller.edu <mailto:ppolosecki@mail.rockefeller.edu> <mailto:ppolosecki@mail.rockefeller.edu <mailto:ppolosecki@mail.rockefeller.edu>> <mailto:ppolosecki@mail.rockefeller.edu <mailto:ppolosecki@mail.rockefeller.edu> <mailto:ppolosecki@mail.rockefeller.edu <mailto:ppolosecki@mail.rockefeller.edu>>> <mailto:ppolosecki@mail.rockefeller.edu <mailto:ppolosecki@mail.rockefeller.edu> <mailto:ppolosecki@mail.rockefeller.edu <mailto:ppolosecki@mail.rockefeller.edu>> <mailto:ppolosecki@mail.rockefeller.edu <mailto:ppolosecki@mail.rockefeller.edu> <mailto:ppolosecki@mail.rockefeller.edu <mailto:ppolosecki@mail.rockefeller.edu>>>> ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. 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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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html