[Neuroimaging] [nipype] updated external mask handling in SPM

[Dimitri Papadopoulos Orfanos]

Hi Satra,

I understand the whole purpose of this piece of code is to get SPM to
use an explicit mask. This is done by manipulating the masking structure
"SPM.xM".

I'm not yet entirely convinced this still needs to be done "behind the
back of SPM" by modifying SPM.mat outside of the SPM code, but here is
one of "John's Gems" that recommends this Nipype hack (it refers to SPM2
though):
  http://blogs.warwick.ac.uk/nichols/entry/spm2_gem_12/

  With fMRI data/models, SPM2 is fully capable of doing explicit
  masking, but the user interface for fMRI doesn't ask for it.
  One way to do this type of masking anyway is to change the
  SPM.mat file *after* you specify your model, but *before*
  clicking 'Estimate'.
  Specifically:
     1. Load the SPM.mat file,
               load SPM
        set the SPM.xM.TH values all to -Inf,
               SPM.xM.TH = -Inf*SPM.xM.TH;
        and, in case that you have an image format not allowing
        NaNs, set SPM.xM.I to 0
               SPM.xM.I = 0;
     2. If using a mask image, set SPM.xM.VM to a vector of
        structures, where each structure element is the output
        of spm_vol. For instance:
               SPM.xM.VM = spm_vol('Maskimage');
     3. Finally, save by
               save SPM SPM


Most importantly, I am puzzled by the fact that we don't find the same
results when running SPM8 via Nipype than when running SPM8 back in
2010-2012 using batches created from the SPM user interface. At this
point I am not sure if this is an issue with Nipype, an issue with our
own scripts created in 2009-2010, or perhaps related to changes in SPM8.
I would like to the bottom of it - time permitting... I don't feel
comfortable with the idea that the default SPM workflow could have been
modified and I'd like to understand the cause of the discrepancy in the
results.

Best,
Dimitri

Le 02/12/2015 23:17, Satrajit Ghosh a écrit :
> hi dimitri,
> 
> it's been a long while since those lines were written. but i believe
> this was written as noted in the comments to support the case where the
> user simply wanted spm to use the explicit mask. the other reason for it
> was that there were several places that could control spm options (e.g.,
> config file). we did not want to rely on the config file.
> 
> i believe it was more of a perspective on what an explicit mask meant. i
> can't remember if this was discussed on the spm list or came from best
> practices in our lab at that time.
> 
> cheers,
> 
> satra
> 
> On Wed, Dec 2, 2015 at 9:45 AM, Dimitri Papadopoulos Orfanos
> <dimitri.papadopoulos at cea.fr <mailto:dimitri.papadopoulos at cea.fr>> wrote:
> 
>     Hi,
> 
>     I have a question on the following commit:
>     https://github.com/nipy/nipype/commit/fe9d0e07a288afefb34e99f488ef194a443d6089
> 
>     Could someone explain the rationale behind the addition of this piece of
>     code in nipype/interfaces/spm/model.py? We came across this code while
>     trying to reproduce the results obtained with an old version of SPM8 run
>     manually vs. the latest version of SPM8 run from Nipype.
> 
>             if isdefined(self.inputs.mask_image):
>                 # SPM doesn't handle explicit masking properly, especially
>                 # when you want to use the entire mask image
>                 postscript = "load SPM;\n"
>                 postscript += "SPM.xM.VM = spm_vol('%s');\n" %
>     list_to_filename(self.inputs.mask_image)
>                 postscript += "SPM.xM.I = 0;\n"
>                 postscript += "SPM.xM.T = [];\n"
>                 postscript += "SPM.xM.TH <http://SPM.xM.TH> =
>     ones(size(SPM.xM.TH <http://SPM.xM.TH>))*(%s);\n" %
>     self.inputs.mask_threshold
>                 postscript += "SPM.xM.xs = struct('Masking', 'explicit
>     masking only');\n"
>                 postscript += "save SPM SPM;\n"
> 
>     We have understood almost all causes for differences in results. The
>     only cause that remains to be explained is this Nipype hack. Has perhaps
>     this issue been discussed on the SPM mailing list?
> 
>     Best,
>     --
>     Dimitri Papadopoulos
>     CEA/Saclay
>     I2BM, NeuroSpin
>     F-91191 Gif-sur-Yvette cedex, France
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> 
> 
> 
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