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