Hi Colin,
in spm_defaults.m there is a field defaults.mask.thresh somewhere which is set at 0.8 (80%) of total in brain signal intensity. I often have to lower it as well for some special sequences that have lower intensities at the edges. Also for strong smoothing you might need lower values. I actually put it on 0.2 by default, even for normal EPI sequences, to my taste too much signal gets masked out for the default setting of 0.8.
When you lower it, of course you need to be cautious for out of brain activation in artifactual signal, for example caused by nyquist ghosting or in non-neuronal tissue.
I think it is about time this threshold is moved to the batch tree GUI for everyone to edit and save. I've seen to many posters and papers already where suspiciously large edges of the cortex are blanked from activation maps, clearly visible in an overlay on a T1 template. I guess many people uncorrectly take this default threshold for granted, which might not be a good idea.
Who knows how many interesting science about the function of outer gyral crowns and lips has gone down the drain ;-)
Cheers,
Bas
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Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
Visiting : Heidelberglaan 100, 3584 CX Utrecht
Room B.01.1.03
Mail : Huispost B01.206, P.O. Box 85500
3508 GA Utrecht, the Netherlands
Tel : +31 (0)88 7559609
Fax : +31 (0)88 7555443
E-mail : [log in to unmask]
Web : http://www.neuromri.nl/people/bas-neggers
: http://www.brainsciencetools.com (CEO)
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________________________________________
From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Colin Shaun Hawco, M [[log in to unmask]]
Sent: Wednesday, August 22, 2012 11:47 PM
To: [log in to unmask]
Subject: [SPM] Low signal voxels being masked out
Hello all,
I am having a problem with voxels being masked out of my analysis due to lower signal. I have some extra equipment inside the scanner which causes a bit of increased signal loss. However, when I look at my actual functional data (preprocessed or not preprocessed), the signal loss is not that severe.
I am running a fairly standard HRF analysis, with implicit masking off and no mask specified. I'm loosing a LOT of data from signal loss, in the usual regions (anterior temporal and medial frontal). When I load the Beta or contrast images, there is simply no data in those regions. But looking at the raw data, their appears to be enough signal for a reasonable analysis. The signal loss in some cases even extends into the hippocampus and medial temporal structures, which seems very excessive to me.
I wan to force SPM to do statistics on those voxels. I can see no option at present to allow such a thing. Is there any way for me to force SPM to calculate statistics for those regions, and not engage in this (unasked for) implicit masking?
Thanks for the help.
Colin.
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