That's true, it didn't look good. Did that patient have a stroke in the past? That could be causing some issues.
It might be best if you manually reorient the T1 and the EPI's so that the origin (0 0 0) is roughly at the anterior commissure. This should help both coreg and segmentation.
Chris


han zhang wrote:

Hi Marta,
 What I saw in addition is the coregistration result is not good enough.
See from the pdf file, the EPI image was not coregistered to the T1 image, maybe the scalp was too bright and you should use BET before coreg?
 Could this also explain the posterior activation from what you expected?
 Han

 2010/8/27 Gandolla Marta <[log in to unmask] <mailto:[log in to unmask]>>

   well, sorry for bothering you all again...
   my concern is that quite everyone in literature uses realignment
   parameters as covariats of no interest... do you think it is ok
   not to use them?
   thanks for the help
   marta

   2010/8/26 Chris Watson <[log in to unmask]

   <mailto:[log in to unmask]>>

       Don't include motion parameters as regressors.

       I'm sure you already do this, but I've seen that it's good to
       have a practice session outside of the scanner to see how much
       they move when doing the task. Then you can coach them into
       trying to move their body less. Also, putting some pillows
       under their knees, so their feet are elevated, helps quite a
       bit. And of course vacuum bags, tape across the forehead, etc.

       Gandolla Marta wrote:

           Hi Chris and list,
              so, what do you suggest?

           2010/8/26 Chris Watson
           <[log in to unmask]
           <mailto:[log in to unmask]>

           <mailto:[log in to unmask]
           <mailto:[log in to unmask]>>>

              I think that for something as simple as ankle
           dorsiflexion, if the
              results are in a plausible location, you can believe
           them. The
              motion really isn't that bad. It's hard to keep a
           patient still
              when doing foot movements, so there will probably always be
              stimulus-correlated motion, and if you include the motion
              parameters as regressors (as you have seen already),
           it'll get rid
              of any true activation.

              Gandolla Marta wrote:

                  Hi Chris and everyone else!!
                    indeed, we are looking at right ankle
           dorsiflexion and yes,
                  I definitively agree that the activation seems to
           be quite
                  posterior.
                  the graph I posted has on x axis the number of scan
           (TR=3secs,
                  5 minutes of acquisition). on the y axis there are
           mm for
                  blue, green and d line, and degrees for yellow,
           cyan and
                  magenta line. I superimposed all the realignemnt
           parameters
                  along with the block design to search for the eventual
                  correlation. I attached in any case te SPM output
           of realignment.

                  all my best
                  marta
                  2010/8/26 Chris Watson
                  <[log in to unmask]
           <mailto:[log in to unmask]>
                  <mailto:[log in to unmask]
           <mailto:[log in to unmask]>>
                  <mailto:[log in to unmask]
           <mailto:[log in to unmask]>
                  <mailto:[log in to unmask]
           <mailto:[log in to unmask]>>>>


                     Is it right ankle dorsiflexion that you're
           looking at?
                     It looks pretty posterior to the motor strip;
           what does it look
                     like overlaid on a structural?
                     What's the scale (units) of the graph you
           posted? Can you
                  post the
                     output of SPM's realignment?


                     Gandolla Marta wrote:

                         Hi everyone,
                            I attached a pdf file instead of a docx
           of the previous
                         e-mail. sorry for the inconvenience!!
                            I'd need some help about realignment
           parameters
                  effect that
                         seems to be huge in the acquisition I will
           now describe.
                         We have a 30 secs block design, starting
           from rest. The
                         patient is performing active ankle
           dorsiflexion during
                  on blocks.
                         We did the following preprocessing steps:
                         - realignment
                         - coreg
                         - normalize
                         - smooth (6mm)
                          then we implemented the GLM with a 8
           columns design matrix
                         (1-condition with the 30 secs block design,
           2-7- realign
                         param, 8- baseline) and we found zero activation
                  (p<0.01 FWE
                         corrected).
                         we then chacked with the 2 columns design matrix
                  (1-condition
                         with the 30 secs block design, 2- baseline)
           and we found a
                         quite important activation (fig.1). should
           we trust this
                         activation? the realignemnt param plot along
           with the block
                         design protocol is shown in fig.2. is it
           possible that all
                         this effect depends on the correlation
           between the
                  realignment
                         parameters and the condition column in the
           design matrix?
                         should trust only the design with the
           realignement
                  parameters
                         as covariats of no interest? we are thinking
           in this
                  case why
                         we don't see any activation... do we miss
           something?
                          thanks for your help
                         best regards
                         marta







--
Han ZHANG
NeuoImage Computing (NIC) group
http://psychbrain.bnu.edu.cn/home/chaozhezhu/
http://publicationslist.org/han_zhang
State Key Lab of Cognitive Neuroscience and Learning
Beijing Normal Univ 19# Xinjiekouwai St. 100875, Beijing, China
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