Hello, I'm trying to display some FEAT statistics on a surface I created using Freesurfer using instructions from http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html. The automatic registration function reg-feat2anat seems to have failed and I'm not sure what I should do to re-orient the slices better. I've attached a picture, hopefully it will convey my problem.
Also, looking at the log files, I noticed the line INFO: could not find /home/eleung1/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/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file Where do I get the file avg152T1_brain.mat? Thanks for your help, Elaine
<<attachment: n002_registration.jpg>>
Tue Feb 20 11:42:45 EST 2007 /home/eleung1/freesurfer/subjects /home/eleung1/freesurfer/bin//reg-feat2anat --feat /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat --subject n002 Linux brodmann.bu.edu 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 13:14:25 CDT 2005 i686 i686 i386 GNU/Linux mri_convert /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz mri_convert /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz reading from /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz... TR=2530.00, TE=3.39, TI=1100.00, flip angle=7.00 i_ras = (-1, -8.15313e-11, 3.35233e-10) j_ras = (3.14573e-09, -4.86297e-10, -1) k_ras = (9.86348e-10, 1, 1.31955e-09) writing to /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz... example_func ras_good_flag 1 ------------------------------------------------------- Initializing exf2anat with header tkregister2 --targ /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz --mov /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat.init --fslregout /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.init.fsl.mat --regheader --noedit target volume /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz movable volume /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz reg file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat.init LoadVol 0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 INFO: using NIfTI-1 sform INFO: loading target /home/eleung1/freesurfer/subjects/n002/mri/brain.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/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz INFO: using NIfTI-1 sform Tmov: -------------------- -3.125 0.000 0.000 100.000; 0.000 0.000 2.200 -60.500; 0.000 -3.125 0.000 100.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 ---- Input registration matrix (computed) -------- 1.000 0.000 -0.000 7.451; -0.000 0.000 1.000 -20.153; -0.000 -1.000 -0.000 -59.694; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 -0.000 7.451; -0.000 0.000 1.000 -20.153; -0.000 -1.000 -0.000 -59.694; 0.000 0.000 0.000 1.000; subject = subject-unknown RegMat --------------------------- 1.000 0.000 -0.000 7.451; -0.000 0.000 1.000 -20.153; -0.000 -1.000 -0.000 -59.694; 0.000 0.000 0.000 1.000; register: file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat.init written FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -21.4844, ref det = -1 betfunc /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/exfbet Tue Feb 20 11:42:55 EST 2007 flirt -ref /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/anat.nii.gz -in /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/exfbet.nii.gz -init /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.init.fsl.mat -out /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.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 n002 --mov /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat --fslreg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.fsl.mat --noedit --mgz ---- FSL registration matrix -------- 0.975 0.028 0.220 17.472; 0.087 -0.961 -0.264 254.547; 0.203 0.276 -0.939 103.727; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz reg file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat LoadVol 0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 INFO: using NIfTI-1 sform INFO: loading target /home/eleung1/freesurfer/subjects/n002/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: loading movable /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz INFO: using NIfTI-1 sform Tmov: -------------------- -3.125 0.000 0.000 100.000; 0.000 0.000 2.200 -60.500; 0.000 -3.125 0.000 100.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI_GZ fsl2TkReg: mov det = -21.4844, ref det = -1 ---- Input registration matrix (computed) -------- 0.975 -0.203 0.087 -1.687; -0.220 -0.939 0.264 -25.687; 0.028 -0.276 -0.961 -31.406; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.975 -0.203 0.087 -1.687; -0.220 -0.939 0.264 -25.687; 0.028 -0.276 -0.961 -31.406; 0.000 0.000 0.000 1.000; subject = n002 RegMat --------------------------- 0.975 -0.203 0.087 -1.687; -0.220 -0.939 0.264 -25.687; 0.028 -0.276 -0.961 -31.406; 0.000 0.000 0.000 1.000; register: file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat written tkregister2 --targ /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.img --mov /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz --fslreg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/example_func2standard.mat --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/std2exf.register.dat --noedit ----------------------------------------------------------------- INFO: could not find /home/eleung1/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/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file ----------------------------------------------------------------- ----------------------------------------------------------------- INFO: could not find /home/eleung1/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/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file ----------------------------------------------------------------- ----------------------------------------------------------------- INFO: could not find /home/eleung1/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/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.mat file ----------------------------------------------------------------- ---- FSL registration matrix -------- 0.925 0.038 0.025 -10.083; -0.016 0.373 -1.040 104.961; -0.071 0.914 0.396 -43.195; 0.000 0.000 0.000 1.000; --------------------------------------- target volume /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.img movable volume /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz reg file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/std2exf.register.dat LoadVol 0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 INFO: using NIfTI-1 sform INFO: loading target /home/eleung1/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: loading movable /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz INFO: using NIfTI-1 sform Tmov: -------------------- -3.125 0.000 0.000 100.000; 0.000 0.000 2.200 -60.500; 0.000 -3.125 0.000 100.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI_GZ fsl2TkReg: mov det = -21.4844, ref det = -8 ---- Input registration matrix (computed) -------- 1.078 -0.008 0.048 -2.561; -0.011 -0.832 0.339 -17.144; 0.079 -0.361 -0.944 -36.034; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.078 -0.008 0.048 -2.561; -0.011 -0.832 0.339 -17.144; 0.079 -0.361 -0.944 -36.034; 0.000 0.000 0.000 1.000; subject = subject-unknown RegMat --------------------------- 1.078 0.048 0.008 -2.561; -0.011 0.339 0.832 -17.144; 0.079 -0.944 0.361 -36.034; 0.000 0.000 0.000 1.000; register: file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/std2exf.register.dat written mri_matrix_multiply -fsl -im /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.fsl.mat -iim /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/example_func2standard.mat -om /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/std2anat.fsl.mat ------------------------------------------------------- tkregister2 --targ /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz --mov /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2std.register.dat --fslreg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/std2anat.fsl.mat --noedit ---- FSL registration matrix -------- 1.056 -0.165 0.055 47.751; 0.016 -0.127 -1.000 224.821; 0.230 0.883 -0.068 10.423; 0.000 0.000 0.000 1.000; --------------------------------------- target volume /home/eleung1/freesurfer/subjects/n002/mri/brain.mgz movable volume /home/eleung1/freesurfer/fsl/etc/standard/avg152T1_brain.img reg file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2std.register.dat LoadVol 0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/eleung1/freesurfer/subjects/n002/mri/brain.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/eleung1/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) -------- 0.908 -0.175 0.038 1.200; -0.044 -0.134 0.988 -7.548; -0.233 -1.077 -0.086 -7.170; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.908 -0.175 0.038 1.200; -0.044 -0.134 0.988 -7.548; -0.233 -1.077 -0.086 -7.170; 0.000 0.000 0.000 1.000; subject = subject-unknown RegMat --------------------------- 0.908 -0.175 0.038 1.200; -0.044 -0.134 0.988 -7.548; -0.233 -1.077 -0.086 -7.170; 0.000 0.000 0.000 1.000; register: file /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2std.register.dat written To visually check your results, run: tkregister2 --s n002 --mov /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/example_func.nii.gz --reg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/anat2exf.register.dat --fslreg /home/eleung1/Vaina/N002/TrioTim-35006-20070211-180738-596000/feat/005_n002-global-fsl.feat/reg/freesurfer/exf2anat.fsl.mat --surf orig --tag Tue Feb 20 11:43:48 EST 2007 reg-feat2anat done
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