What do you mean there was an orientation problem? If you use analyze files, then it relies on the FSL reg to std space being correct. Is it?
uzay emir wrote:
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