Dear Volkmar and Carles,
thank you for your quick replies and for the tips.
I put the images that you have suggested here: https://www.dropbox.com/sh/ldtao4y8oburisn/AABxUqfG-9_emm7TymLbHOWUa?dl=0
The time series STD map doesn't have any obvious artefacts.
The RES image has the highest intensity around the brain stem, and that how it is supposed to be, isn't it?
I also attach the RPV image, it looks quite homogeneous, but I am not sure how to interpret it.
I also used the Browse utility of CheckReg (thank you, Carles, I didn't know about it), and looked at the realigned image time series. I don't think there are any images with artifacts. But it might be that there are some tiny regular stripy intensity changes... though I'm not sure any more. I made a movie out of it (it's 30 sec), could you have a look if you don't mind?
Here is the one with nn interpolation:
https://www.dropbox.com/s/k5gndgqczndko3y/video_nn.mov?dl=0
And the same movie with trilinear interpolation:
https://www.dropbox.com/s/3uqkg090jnhk533/video_tr.mov?dl=0
thank you very much!
Kind regards,
Irina
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From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Volkmar Glauche [[log in to unmask]]
Sent: Wednesday, August 05, 2015 11:18 AM
To: [log in to unmask]
Subject: Re: [SPM] 1st level analysis artifacts
Dear Irina,
I do not have a good explanation for your findings. I have however seen cases where data looked perfectly normal in terms of intensities but parts of each image were noisier than others. Visual inspection, tsdiffana et al of these raw data didn't reveal anything suspicious.
When looking at the data, you should set interpolation to "nearest neighbour" and orientation to "voxel space". In addition to the beta images, you might want to look at the RPV and ResMS images. These tell you about the smoothness of the error estimates and the model fit. Also it might be helpful to compute a standard deviation image of your time series. You can easily do that using ImCalc: select raw or smoothed data, enter "std(X)" as formula, set interpolation to nearest neighbour and "Read data into data matrix" to "Yes".
Instead of using "Display" you might want to use "Check Reg" and look at more than one image at the same time.
Best,
Volkmar
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