[MINC-users] mincresample center offset
Jon Erik Ween
jween at klaru-baycrest.on.ca
Wed Mar 18 23:44:04 EDT 2009
Dear minclist friends
After a resounding victory over the install/configuration issues in my
previous thread, (thanks to help from the list!) I am on to another
newbe issue:
In trying to register a target brain to an atlas, things get offset
(see attached picture), I'm thinking due to something I'm leaving out
about world coordinates in creating the transform. What am I missing?
Cheers
Jon
Soli Deo Gloria
Here is some info:
bash-3.2$ mritoself /usr/local/share/mni_autoreg/
icbm_template_1.00mm_bet.mnc 14017_083005_3dvol_bet.mnc
14017_083005_3dvol
bash-3.2$ mincresample -like /usr/local/share/mni_autoreg/
icbm_template_1.00mm_bet.mnc -transform 14017_083005_3dvol.xfm
14017_083005_3dvol_bet.mnc 14017_083005_3dvol_bet_icbm
MNI Transform File
%Wed Mar 18 22:51:14 2009>>> /usr/local/mni/bin/minctracc /var/folders/
Ph/Ph06bhfiHDWHUvQMhNTgJE++Hbs/-Tmp-/mritoself_7413//
icbm_template_1.00mm_bet_crop.mnc /var/folders/Ph/
Ph06bhfiHDWHUvQMhNTgJE++Hbs/-Tmp-/
mritoself_7413//14017_083005_3dvol_bet_crop.mnc 14017_083005_3dvol -
est_center -transformation /var/folders/Ph/Ph06bhfiHDWHUvQMhNTgJE+
+Hbs/-Tmp-/mritoself_7413//14017_083005_3dvol_tmp1.xfm -lsq6 -mi -
groups 256 -threshold 1195 0 -step 4.3 4.3 4.3 -simplex 1.5
%(Package mni_autoreg 0.99.3, compiled by acveilleux at mrspc.bic.mni.mcgill.ca
(i686-apple-darwin9.2.2) on Wed Apr 2 13:09:57 EDT 2008)
Transform_Type = Linear;
Linear_Transform =
1 0 0 0
0 1 0 0
0 0 1 0;
bash-3.2$ mincinfo 14017_083005_3dvol_bet.mnc
file: 14017_083005_3dvol_bet.mnc
image: signed__ short -32768 to 32767
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 124 1.4 -84.9295
yspace 256 0.859375 -113.669
xspace 256 0.859375 -109.571
bash-3.2$ mincinfo 14017_083005_3dvol_bet_icbm.mnc
file: 14017_083005_3dvol_bet_icbm.mnc
image: signed__ short -32768 to 32767
image dimensions: zspace yspace xspace
dimension name length step start
-------------- ------ ---- -----
zspace 181 1 0
yspace 217 1 0
xspace 181 1 0
Jon Erik Ween, MD, MS
Scientist, Kunin-Lunenfeld Applied Research Unit
Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre
Assistant Professor, Dept. of Medicine, Div. of Neurology
University of Toronto Faculty of Medicine
Kimel Family Building, 6th Floor, Room 644
Baycrest Centre
3560 Bathurst Street
Toronto, Ontario M6A 2E1
Canada
Phone: 416-785-2500 x3648
Fax: 416-785-2484
Email: jween at klaru-baycrest.on.ca
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