Thank you,it is working now. However, I have anorientation problem
with automatic registration results. This problem has been mentioned
before but i could not find any reply. I think this is something
related following lines where I found it in the reg- feat2anat log file.
Regards
Uzay
----------------------------------------------------------------- INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file ----------------------------------------------------------------- INFO: using NIfTI-1 sform
----------------------------------------------------------------- INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file ----------------------------------------------------------------- ----------------------------------------------------------------- INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
__________________________________________________
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------------------------------------------------------------------------
Fri May 18 11:13:12 EEST 2007
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig
/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat
--feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya
Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005
i686 i686 i386 GNU/Linux
mri_convert
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz
mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz
$Id: mri_convert.c,v 1.141 2007/04/26 05:31:21 greve Exp $
reading from
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz...
TR=11.00, TE=4.92, TI=4.92, flip angle=15.00
i_ras = (-1, 2.56273e-11, 6.83856e-10)
j_ras = (-1.17877e-09, -2.94451e-16, -1)
k_ras = (3.0538e-12, 1, -9.84868e-13)
writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...
example_func ras_good_flag
-------------------------------------------------------
Initializing exf2anat from crude std2anat
tkregister2 --targ
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit
target volume
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
movable volume
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
reg file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat
LoadVol 0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
Tmov: --------------------
-2.000 0.000 0.000 91.000;
0.000 0.000 2.000 -91.000;
0.000 -2.000 0.000 109.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 1, float2int = 0
Computing reg from header (and possibly input matrix)
---- Input registration matrix (computed) --------
1.000 0.000 0.000 1.414;
-0.000 -0.000 1.000 -30.612;
0.000 -1.000 -0.000 -44.496;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
1.000 0.000 0.000 1.414;
-0.000 -0.000 1.000 -30.612;
0.000 -1.000 -0.000 -44.496;
0.000 0.000 0.000 1.000;
subject = subject-unknown
RegMat ---------------------------
1.000 0.000 0.000 1.414;
-0.000 -0.000 1.000 -30.612;
0.000 -1.000 -0.000 -44.496;
0.000 0.000 0.000 1.000;
register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat
written
FSLOUTPUTTYPE NIFTI_GZ
tkreg2FSL: mov det = -8, ref det = -1
mri_matrix_multiply -fsl -bin -iim
Akkaya_Zuhre_1_9++.feat//reg/example_func2standard.mat -iim
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat -om
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.init.fsl.mat
betfunc Akkaya_Zuhre_1_9++.feat//example_func
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/exfbet
Fri May 18 11:13:24 EEST 2007
flirt -ref Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz -in
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/exfbet.nii.gz -init
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.init.fsl.mat -out
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6
-searchrx -90 90 -searchry -90 90 -searchrz -90 90
WARNING: Both reference and input images have an sform matrix set
The output image will use the sform from the reference image
-------------------------------------------------------
tkregister2 --s akkaya --mov Akkaya_Zuhre_1_9++.feat//example_func.nii.gz --reg
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat --fslreg
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.fsl.mat --noedit --mgz
---- FSL registration matrix --------
0.009 -0.924 -0.383 227.568;
-0.306 0.362 -0.880 150.574;
0.952 0.125 -0.279 20.398;
0.000 0.000 0.000 1.000;
INFO: using NIfTI-1 sform
---------------------------------------
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume Akkaya_Zuhre_1_9++.feat//example_func.nii.gz
reg file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat
LoadVol 0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig.mgz
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: using NIfTI-1 sform
INFO: loading movable Akkaya_Zuhre_1_9++.feat//example_func.nii.gz
Tmov: --------------------
-3.000 0.000 0.000 96.000;
0.000 0.000 3.750 -67.500;
0.000 -3.000 0.000 96.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI_GZ
fsl2TkReg: mov det = -33.75, ref det = -1
---- Input registration matrix (computed) --------
0.009 -0.952 -0.306 -12.434;
0.383 -0.279 0.880 -39.490;
-0.924 -0.125 0.362 -1.258;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
0.009 -0.952 -0.306 -12.434;
0.383 -0.279 0.880 -39.490;
-0.924 -0.125 0.362 -1.258;
0.000 0.000 0.000 1.000;
subject = akkaya
RegMat ---------------------------
0.009 -0.952 -0.306 -12.434;
0.383 -0.279 0.880 -39.490;
-0.924 -0.125 0.362 -1.258;
0.000 0.000 0.000 1.000;
register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat
written
tkregister2 --targ
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --mov
Akkaya_Zuhre_1_9++.feat//example_func.nii.gz --fslreg
Akkaya_Zuhre_1_9++.feat//reg/example_func2standard.mat --reg
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2exf.register.dat --noedit
---- FSL registration matrix --------
1.023 -0.007 0.032 -12.177;
-0.001 1.201 0.148 -1.616;
-0.014 -0.173 1.167 18.642;
0.000 0.000 0.000 1.000;
-----------------------------------------------------------------
INFO: could not find
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for
direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
INFO: using NIfTI-1 sform
-----------------------------------------------------------------
INFO: could not find
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for
direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
-----------------------------------------------------------------
INFO: could not find
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for
direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
---------------------------------------
target volume
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
movable volume Akkaya_Zuhre_1_9++.feat//example_func.nii.gz
reg file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2exf.register.dat
LoadVol 0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: using NIfTI-1 sform
INFO: loading movable Akkaya_Zuhre_1_9++.feat//example_func.nii.gz
Tmov: --------------------
-3.000 0.000 0.000 96.000;
0.000 0.000 3.750 -67.500;
0.000 -3.000 0.000 96.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI_GZ
fsl2TkReg: mov det = -33.75, ref det = -8
---- Input registration matrix (computed) --------
0.977 -0.002 0.027 -3.080;
-0.012 0.121 0.841 7.974;
-0.000 -0.817 0.104 13.120;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
0.977 -0.002 0.027 -3.080;
-0.012 0.121 0.841 7.974;
-0.000 -0.817 0.104 13.120;
0.000 0.000 0.000 1.000;
subject = subject-unknown
RegMat ---------------------------
0.977 0.027 0.002 -3.080;
-0.012 0.841 -0.121 7.974;
-0.000 0.104 0.817 13.120;
0.000 0.000 0.000 1.000;
register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2exf.register.dat
written
mri_matrix_multiply -fsl -im
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.fsl.mat -iim
Akkaya_Zuhre_1_9++.feat//reg/example_func2standard.mat -om
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat
-------------------------------------------------------
tkregister2 --s akkaya --targ
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslreg
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --noedit
---- FSL registration matrix --------
0.005 -0.801 -0.227 230.557;
-0.309 0.189 -0.770 161.466;
0.927 0.070 -0.273 36.893;
0.000 0.000 0.000 1.000;
---------------------------------------
target volume
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
movable volume
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
reg file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat
LoadVol 0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
Ttarg: --------------------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
Tmov: --------------------
-2.000 0.000 0.000 91.000;
0.000 0.000 2.000 -91.000;
0.000 -2.000 0.000 109.000;
0.000 0.000 0.000 1.000;
mkheaderreg = 0, float2int = 0
FSLOUTPUTTYPE NIFTI_GZ
fsl2TkReg: mov det = -8, ref det = -1
---- Input registration matrix (computed) --------
0.004 -0.964 -0.343 -7.962;
0.287 -0.361 1.086 -58.034;
-1.166 -0.108 0.305 -10.228;
0.000 0.000 0.000 1.000;
---------------------------------------
---- Input registration matrix --------
0.004 -0.964 -0.343 -7.962;
0.287 -0.361 1.086 -58.034;
-1.166 -0.108 0.305 -10.228;
0.000 0.000 0.000 1.000;
subject = akkaya
RegMat ---------------------------
0.004 -0.964 -0.343 -7.962;
0.287 -0.361 1.086 -58.034;
-1.166 -0.108 0.305 -10.228;
0.000 0.000 0.000 1.000;
register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat
written
To visually check your results, run:
tkregister2 --s akkaya --mov Akkaya_Zuhre_1_9++.feat//example_func.nii.gz --reg
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat --fslreg
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.fsl.mat --surf orig --tag
Fri May 18 11:14:51 EEST 2007
reg-feat2anat done
