Thanks for your suggestion James.
I was just reminded that Caret5 has an option to convert "NaNs" in a
volume to zero.
1) Start Caret5.
2) Load the volume as the desired type, most likely functional in this
case.
3) Select Mathematical Operations from the Volume Menu.
4) For Volume A, set the type to functional (type used for loading the
volume in step 2) and make sure Volume FIle is set to the volume loaded
in step 2.
5) Set the Output Volume as desired. It is probably best to use New
Volume so that a new volume is created.
6) Set the operation to to "Fix Nan (Not a Number) in Volume A.
7) Press the Apply Button.
8) Save the newly created volume using the File Menu's Save Data File.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Jul 25, 2005, at 3:55 PM, Jim Thompson wrote:
Hi John, Uma
This should do it:
taken from http://www.sph.umich.edu/~nichols/JohnsGems.html#Gem2
in matlab type (with adjusted filenames):
VI = spm_vol('original_beta.img');
VO = VI;
VO.fname = 'patched_beta.img';
VO = spm_create_image(VO);
for i=1:VI.dim(3),
img = spm_slice_vol(VI,spm_matrix([0 0
i]),VI.dim(1:2),0);
tmp = find(isnan(img));
img(tmp) = 0;
VO = spm_write_plane(VO,img,i);
end;
Jim
-----------------------------------------------------------------------
-
James C. Thompson, PhD
Research Associate
Center for Advanced Imaging
Department of Radiology
West Virginia University
Robert C Byrd Health Sciences Center South
PO Box 9235
Morgantown WV 26506-9235
USA
Tel: +1 304 293 5050
Fax: +1 304 293 4287
email: [EMAIL PROTECTED]
-----------------------------------------------------------------------
-
[EMAIL PROTECTED] 07/25/05 4:44 PM >>>
Hi Uma,
I am not familiar with the "beta" and "con" volumes. However, when I
searched google, I found a couple of web pages that state that in the
"beta" and "con" volumes, voxels outside the brain are set to Nan (not
a number).
The web page "http://psyphz.psych.wisc.edu/~oakes/spm/spm_how_tos.html";
states " One caveat which you may know if you've followed the list, is
that the con**.img and beta*.img images have the areas outside the
brain values set
to NaN".
Something similar to this is posted on the SPM99 web site
"http://www.fil.ion.ucl.ac.uk/spm/software/spm99/"; that voxels outside
the brain are set to 0 or Nan.
Caret5 expects all voxels in a volume to have valid numerical values.
You will need to find a way to convert the NaN voxels to zeros in your
volumes.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Jul 25, 2005, at 1:08 PM, Uma Sreekumar wrote:
Hi all,
I am new to Caret. I am trying to map results of my
group level analysis performed in SPM99 onto the PALS
atlas in Caret 5.3.
While I am able to map the spmT*.hdr for the
functional volume (as per the online documentation
provided), I am unable to map the con*.hdr or
beta*.hdr. Following around 80% processing, wherein
both the scaling and descaling ranges are read as -NaN
-NaN, the programme crashes with the message
sqrt: domain error.
All required settings (voxel size etc) seem to be
correct. I have gone through the previous mails in the
list. Shouldnt it be possible to map any SPM *.hdr
file through Caret? Help of any kind would be highly
appreciated.
Best regards,
Uma Sreekumar
-----------------------------
Y. Uma Sreekumar
NMR Research Centre,
Institute of Nuclear Medicine and Allied Sciences,
Delhi- 110 054, INDIA
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