Hi all,

Just for the record I comment that the problem was solved. It was the name of the sequence, which containted the sting "TR". This messed up the sanity checks mkanalysis-sess. Thank you very much taking a look at it.
Best,
Pablo

On Fri, Feb 18, 2011 at 5:48 PM, Pablo Polosecki <ppolosecki@mail.rockefeller.edu> wrote:
Hi,
The full terminal  output is pretty much what I sent previously:

Processing analysis: a1u
INFO:  analysis a1u exists, but overwrite forced by user.

Setting TER to .10000000000000000000
/home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy
ERROR: bad format for seq.info file, /home/ppolosecki/space/data/ppolosecki/cooked/2011/110211Quincy


Is there a log file that the command spits out and I should send?

Best,
Pablo



On Fri, Feb 18, 2011 at 5:32 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
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>>
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              <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
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       <mailto:ppolosecki@mail.rockefeller.edu>>>>

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MGH-NMR Center
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