That's exactly the news I was hoping for!

Thanks,
Doug


-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
Behalf Of Douglas Burman
Sent: Saturday, June 03, 2006 13:18
To: [log in to unmask]
Subject: Re: [SPM] SPM mask import w/ multiple distinct regions each w/ a
different value??


Jeff,

If you can convert your ITK-SNAP mask to the Analyze format, you can use
SPM's ImCalc to convert the mask into the binary format used by SPM masking
procedures. ImCalc can be used to select any combination of regions from
your mask by specifying whether you are selecting voxels with values greater
than 0, equal to some specified value, or within a range of values. You can
find the syntax for ImCalc in the Help section of SPM (or by searching the
archives).

Hope this helps.

Doug

On Fri, 02 Jun 2006 1:45:08 pm CDT Jeff Browndyke wrote:

Thanks for responding, Volkmar.

The reason I was asking is due to the manual segmentation output afforded by
a program we are using for that purpose; ITK-SNAP. ITK-SNAP will allow for
multiple segments in the same mask with each one assigned a different mask
value (i.e., left hippocampus = 1, right hippocampus = 2, etc.). Since our
subjects are going to have at least 8 ROIs per subject, I was hoping that
there was a way we could keep all the segments in the same mask file, but
trick SPM2 into only recognizing mask values associated with an individual
regions (i.e., apply mask, but only recognize masked region with value = 1
and then reapply the mask to only recognize masked region with value = 2,
and so on). If we have to come up with separate masks for each region
that's o.k., but I was hoping to keep them together for subsequent
visualization purposes as ITK-SNAP does a nice job of 3D visualization and
separate color-coding of each segmented region. Unfortunately, ITK-SNAP
does not allow one to merge masks, so the decision to go one way or the
other (i.e., individual 1/0 masks vs. multiple value masks) will need to be
determined on the frontend.

Regards,
Jeff


-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On
Behalf Of Volkmar Glauche
Sent: Friday, June 02, 2006 02:51
To: [log in to unmask]
Subject: Re: [SPM] SPM mask import w/ multiple distinct regions each w/ a
different value??


Jeff,

I don't know what you want to do with this mask, but probably you need to
have separate masks for each individual region.

Volkmar

On Thu, 1 Jun 2006, Jeff Browndyke wrote:

> Is it possible to import into SPM a mask that has different values for
> distinct mask regions (i.e., value 1 = 1eft hippocampus, value 2 =
> right hippocampus, etc.)? Or, am I relegated to constructing separate
> binary masks for each structure and applying each one sequentially to the
data?
>
> Jeff
>
>

--
Volkmar Glauche
-
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg

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