[MINC-users] mincresample center offset

[Jon Erik Ween]

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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