On 09/25/2006 11:16 PM, DG MCLAREN wrote:
Yes, this can be done. There is paper that is under review that contains
this process in article format; however, I'll write the procedure below:
1) Create individual ROIs for each individual participant using their
own fiducial surface (I'm assuming you've done this already).
2) When you run the deformation (surface --> deformation --> apply
deformation; make sure you check the nearest neighbor option. Now the
deformed data, in standard space of 73730 nodes will be binary coded.
3) Under Attributes --> Metric --> Mathematical Operations; you can add
up the binary files to look at overlap on the average fiducial surface.
This is an excellent way to view the overlap.
Also be aware that AFNI/SUMA has some nice command line utilities that
can save time when you have a bunch of files to sum. This command shows
how I summed a bunch of binary volumes from the Zilles lab to make some
probabilistic maps:
3dcalc -expr a+b+c+d+e+f+g+h+i+j+k+l -prefix
wu_n=12_Brodmann_2_b_lin2StdMNI -a
wu_pm14686_Brodmann_2_b_lin2StdMNI+orig.HEAD -b
wu_pm1696_Brodmann_2_b_lin2StdMNI+orig.HEAD -c
wu_pm18992_Brodmann_2_b_lin2StdMNI+orig.HEAD -d
wu_pm20784_Brodmann_2_b_lin2StdMNI+orig.HEAD -e
wu_pm2431_Brodmann_2_b_lin2StdMNI+orig.HEAD -f
wu_pm28193_Brodmann_2_b_lin2StdMNI+orig.HEAD -g
wu_pm295_Brodmann_2_b_lin2StdMNI+orig.HEAD -h
wu_pm34083_Brodmann_2_b_lin2StdMNI+orig.HEAD -i
wu_pm38281_Brodmann_2_b_lin2StdMNI+orig.HEAD -j
wu_pm5694_Brodmann_2_b_lin2StdMNI+orig.HEAD -k
wu_pm6895_Brodmann_2_b_lin2StdMNI+orig.HEAD -l
wu_pm7186_Brodmann_2_b_lin2StdMNI+orig.HEAD
I haven't done this with metric/shape files, but if I needed to, I'd
consider using AFNI's 1deval for this purpose. (Using shell scripts,
you'd need to strip the header and node numbers and put them back on,
but this isn't too hard to do.)
If you would like more detailed instructions, or the paper reference;
please contact me at [EMAIL PROTECTED]
Best Regards, Donald McLaren
=====================
D.G. McLaren
University of Wisconsin - Madison
Neuroscience Training Program
Tel: (773) 406 2464
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----- Original Message -----
From: Akiko Ikkai <[EMAIL PROTECTED]>
Date: Monday, September 25, 2006 6:07 pm
Subject: [caret-users] Assigning binary to ROI
To: caret-users@brainvis.wustl.edu
Hello,
I'm trying to project ROI masks (where voxels in ROI= 1, outside
ROI= 0)
onto a deformed surface. ROIs are in .hdr/img format, and the
origin is
set at AC. I use "attributes > map volume to surface" to make metric
files, each of which contains just one ROI (e.g. L_FEF.metric,
L_IPS.metric, etc...). Then "surface > deformation > apply deformation
map" to create deformed metric file.
Since the original ROI masks are binary, I'd like to rewrite the
metricfile in binary as well (anything above 0 -> 1). Is there any
way to do
this in caret? If not, is there anyway to get to the .hdr file that is
enbedded in .metric file to binarise? My goal is to create binary ROIs
for each subject, overlay and see the degree of overlap across
subjects.
Thanks in advance.
Akiko Ikkai
PhD Candidate
Department of Psychology
New York University
6 Washington Place New York NY, 10003
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Donna L. Dierker
(Formerly Donna Hanlon; no change in marital status -- see
http://home.att.net/~donna.hanlon for details.)
