Thanks Kathy.
I'm not using spm2 to display spm5 output. The problem is that pickatlas in
spm5 writes left side ROI to the right side (the same shape but just in the
opposite side). And this was verified after I loaded them in mricro,
mricron, and in Matlab. My version is 03-Aug-2006. I'll download the latest
version and see what will happen.
---------------------------------------------
Ze Wang, Ph. D
Center for functional neuroimaging,
Dept of Neurology,
Medicine school,
University of Pennsylvania
3400 Spruce Stree,
3W Gates building,
Philadelphia, PA 19104
Tel: 215-662-7341
-----Original Message-----
From: Kathy Pearson [mailto:[log in to unmask]]
Sent: Tuesday, October 30, 2007 9:57 AM
To: zewang; [log in to unmask]
Subject: RE: [SPM] spm5 +pickatlas orientation problem. totally opposite to
that of spm2
Dr. Wang,
If you use SPM2 to look at SPM5 NIFTI output, the origin will not be
usable due to the switch away from SPM2 Analyze format. This seems
unrelated to WFU_PickAtlas. However, you can look at SPM2 output in
SPM5.
MRIcro ignores the .mat file generated by SPM2. Depending on your
spm.defaults.analyze.flip setting, you may have to manually flip
left/right in MRIcro to match the SPM2 display of the same Analyze file.
This should not be necessary for SPM5 NIFTI output. MRIcron will also
read SPM5 NIFTI format if image data is not stored as double.
Please be sure that you are running the latest version 2.4 of
WFU_PickAtlas. It is available here from the Software Downloads link:
http://www.fmri.wfubmc.edu
I'll write you a separate e-mail message with details about forwarding
an example to me for testing.
Kathy Pearson
WFUHS Radiology
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
On Behalf Of zewang
Sent: Monday, October 29, 2007 3:29 PM
To: [log in to unmask]
Subject: [SPM] spm5 +pickatlas orientation problem. totally opposite to
that of spm2
Dear experts,
I met the orientation nightmare again in spm5. When I use pickatlas
to
generate a ROI (left hippocampus) file, I got output images with totally
different orientations. The one from spm2 is correct (left is left using
spm2 spm5 display or checking with mricro), but that from spm5 is
flipped
(left is on the right using spm display function or checking with
mricro).
Why could this happen? Is it a problem of pickatlas?
Another question is that, without touching any settings and changing the
orientation of the data in spm5, what is the right orientation in spm5's
figure panel?
Thank you very much!
---------------------------------------------
Ze Wang, Ph. D
Center for functional neuroimaging,
Dept of Neurology,
Medicine school,
University of Pennsylvania
3400 Spruce Stree,
3W Gates building,
Philadelphia, PA 19104
Tel: 215-662-7341
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