[MINC-users] mincsample mask problems

[Dylan David Wagner]

	Hi,

          I've finally gotten around to using the -mask feature in 
mincsample to extract all voxel values and coords within a mask.

ie: mincsample -mask average12_hippo.mnc -coords s1_multi_tal_t.mnc

Which would, if I understand the program, give me the voxel values and 
coordinates of all voxels in my tstat file that lie inside the 
hippocampus mask I painted.

However I get the following error: Files average12_hippo.mnc and 
s1_multi_tal_t.mnc have different sizes of dimensions.

      My mask file has a voxel size of 1x1x1 and the fmri file has 
2x2x2. So I resample the mask to 2x2x2 but that didn't help.

      The mask was painted on the anatomical mri (for obvious reasons). 
so while both files are in tal space and now have the same voxel size I 
expect other "dimensions" will remain different. Is there anyway around 
this (short of distorting mask to fit the tstat file's dimensions?).

      Until then it's back to the old way of using minctotag. Which 
doesn't accept masks :(

	(So instead one has to multiply the fmri file by the mask and add a 
constant of say 100. And then get minctotag (modified to output real 
values and not just integers, thanks Jason!) to grab all voxels above 1, 
this way it ignores the 0 voxel values that result from the mask 
multiplication yet it doesn't reject the any negative voxel values in 
the t-stat file (cause they're bumped up by 100). Time consuming to say 
the least, especially as I have to bump them back down by 100 in SPSS to 
get the original values. If anyone knows of other tricks, I'm all ears).


PS: if anyone cares, mincsample compiles for cygwin right out of the 
box! Unlike other apps that I've been unable to compile in cygwin.


		Best,
			DDW


-- 
Dylan David Wagner
Neuropsychology and Cognitive Neuroscience Unit
Montreal Neurological Institute
Tel: (514) 398-4400 (x089722)
Email: dylan.wagner@mail.mcgill.ca
Lab website: http://www.mni.mcgill.ca/cog/jonesgotman/
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