Yes. You can do Realign:Est+Reslice --> Coreg:Est --> Segment -->
Normalise:Write --> Smooth
Did you do Segmentation previously? How did it perform?
Gandolla Marta wrote:
> hi all,
>
> yes, indeed the subject had a srtoke in the past, I thought I
> mentioned it before, but I was wrong.
> I will try to manually reorient the images... should I then run coreg
> and segment, am I right?
>
> thanks a lot
> marta
>
> 2010/8/30 Chris Watson <[log in to unmask]
> <mailto:[log in to unmask]>>
>
> 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]
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>
>
> 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
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>
> 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]
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>
> 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
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> <mailto:[log in to unmask]
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>
> <mailto:[log in to unmask]
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> <mailto:[log in to unmask]
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>
>
> 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
> (Fax) +86-10-5880 6154
> (Tel) +86-10-5880 2965
>
>
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