dt_recon logfile wo 26 okt 2022 11:08:11 CEST VERSION dt_recon 7.3.2 setenv SUBJECTS_DIR /home/ward/freesurfer/subjects/original_data_both_groups cd /home/ward/freesurfer/subjects/testdtrecon /home/ward/freesurfer/bin/dt_recon --i DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.nii --b DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.bval DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.bvec --s NT001_T0_MR_STRUCT --o dti --debug ward-GE72-6QD ward /home/ward/fsl/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input wo 26 okt 2022 11:08:11 CEST cd /home/ward/freesurfer/subjects/testdtrecon mri_convert /home/ward/freesurfer/subjects/testdtrecon/DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.nii /home/ward/freesurfer/subjects/testdtrecon/dti/dwi.nii.gz mri_convert /home/ward/freesurfer/subjects/testdtrecon/DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.nii /home/ward/freesurfer/subjects/testdtrecon/dti/dwi.nii.gz reading from /home/ward/freesurfer/subjects/testdtrecon/DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.nii... TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0266673, -0.998596, 0.0457636) j_ras = (-0.0497214, 0.0470482, 0.997654) k_ras = (0.998407, -0.0243294, 0.0509062) writing to /home/ward/freesurfer/subjects/testdtrecon/dti/dwi.nii.gz... #@#------------------------------- Eddy/Motion Correct wo 26 okt 2022 11:08:16 CEST cd /home/ward/freesurfer/subjects/testdtrecon/dti/ectmp eddy_correct /home/ward/freesurfer/subjects/testdtrecon/dti/dwi.nii.gz /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec.nii.gz 0 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0000 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0001 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0002 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0003 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0004 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0005 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0006 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0007 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0008 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0009 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0010 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0011 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0012 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0013 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0014 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0015 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0016 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0017 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0018 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0019 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0020 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0021 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0022 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0023 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0024 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0025 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0026 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0027 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0028 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0029 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0030 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0031 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0032 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0033 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0034 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0035 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0036 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0037 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0038 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0039 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0040 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0041 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0042 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0043 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0044 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0045 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0046 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0047 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0048 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0049 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0050 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0051 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0052 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0053 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0054 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0055 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0056 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0057 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0058 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0059 processing /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec_tmp0060 #@#------------------------------- Fitting Tensors wo 26 okt 2022 11:10:19 CEST cd /home/ward/freesurfer/subjects/testdtrecon mri_glmfit --y /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec.nii.gz --glmdir /home/ward/freesurfer/subjects/testdtrecon/dti --nii.gz --dti DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.bval DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.bvec 7.3.2 cwd /home/ward/freesurfer/subjects/testdtrecon cmdline mri_glmfit --y /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec.nii.gz --glmdir /home/ward/freesurfer/subjects/testdtrecon/dti --nii.gz --dti DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.bval DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.bvec sysname Linux hostname ward-GE72-6QD machine x86_64 user ward FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec.nii.gz logyflag 1 usedti 1 glmdir /home/ward/freesurfer/subjects/testdtrecon/dti IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/ward/freesurfer/subjects/testdtrecon/dti Loading y from /home/ward/freesurfer/subjects/testdtrecon/dti/dwi-ec.nii.gz ... done reading. Using DTI Loading BValues from DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.bval Found 61 bvalues Loading BVectors from DTI_data_FT_WIPDTI_b1300_d60_MB2_20190706092846_13.bvec Found 61 bvectors Detected BVec file as FSL formatted Saving design matrix to /home/ward/freesurfer/subjects/testdtrecon/dti/Xg.dat Computing normalized matrix Normalized matrix condition is 258.326 Matrix condition is 3.37941e+07 Pruning voxels by thr: 1.175494e-38 Found 263429 voxels in mask Saving mask to /home/ward/freesurfer/subjects/testdtrecon/dti/mask.nii.gz search space = 4116298.500000 Computing natural log of input DOF = 54 Starting fit and test Fit completed in 0.0781333 minutes Writing results Saving DTI Analysis Computing fa Computing ra Computing vr Computing radial diffusivity Computing adc Computing ivc Computing dwisynth Computing dwires Computing dwi rvar mri_glmfit done #@#------------------------------- Registration wo 26 okt 2022 11:10:35 CEST setenv SUBJECTS_DIR /home/ward/freesurfer/subjects/original_data_both_groups cd /home/ward/freesurfer/subjects/testdtrecon bbregister --s NT001_T0_MR_STRUCT --mov /home/ward/freesurfer/subjects/testdtrecon/dti/lowb.nii.gz --init-coreg --lta /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --bold tmp /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299 Log file is /home/ward/freesurfer/subjects/testdtrecon/dti/register.log wo 26 okt 2022 11:10:35 CEST setenv SUBJECTS_DIR /home/ward/freesurfer/subjects/original_data_both_groups cd /home/ward/freesurfer/subjects/testdtrecon /home/ward/freesurfer/bin/bbregister --s NT001_T0_MR_STRUCT --mov /home/ward/freesurfer/subjects/testdtrecon/dti/lowb.nii.gz --init-coreg --lta /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --bold bbregister 7.3.2 Linux ward-GE72-6QD 5.15.0-52-generic #58-Ubuntu SMP Thu Oct 13 08:03:55 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/ward/freesurfer mri_convert /home/ward/freesurfer/subjects/testdtrecon/dti/lowb.nii.gz /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii mri_convert /home/ward/freesurfer/subjects/testdtrecon/dti/lowb.nii.gz /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii reading from /home/ward/freesurfer/subjects/testdtrecon/dti/lowb.nii.gz... TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0266673, -0.998596, 0.0457636) j_ras = (-0.0497214, 0.0470482, 0.997654) k_ras = (0.998407, -0.0243294, 0.0509062) writing to /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii... mri_coreg --s NT001_T0_MR_STRUCT --mov /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii --regdat /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/reg.init.dat --reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /home/ward/freesurfer/subjects/testdtrecon cmdline mri_coreg --s NT001_T0_MR_STRUCT --mov /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii --regdat /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/reg.init.dat --reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname ward-GE72-6QD machine x86_64 user ward dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Seed 53 Reading in mov /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii Reading in ref /home/ward/freesurfer/subjects/original_data_both_groups/NT001_T0_MR_STRUCT/mri/brainmask.mgz Reading in and applying refmask /home/ward/freesurfer/subjects/original_data_both_groups/NT001_T0_MR_STRUCT/mri/aparc+aseg.mgz Setting cras translation parameters to align volume centers Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Init matrix params 1.9934 0.0676 17.5001 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial parameters to be opt 1.9934 0.0676 17.5001 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 93105.0547 mov gstd 1.5249 1.5249 1.5249 Smoothing mov refsat = 116.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0237713730 nhits = 125590 out of 16777216, Percent Overlap: 47.9 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 1.99340; 0.00000 1.00000 0.00000 0.06764; 0.00000 0.00000 1.00000 17.50007; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.01067 -0.01831 -0.39944 99.40232; 0.01989 -0.39906 0.01882 93.44514; -0.39934 -0.02036 -0.00973 83.25284; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -2.00660 -1.93236 -10.49993 2.00000 0.00000 4.00000 -1.0459623 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6: -2.006596 -1.932358 -10.499931 2.000000 0.000000 4.000000 Starting OpenPowel2(), sep = 4 InitialCost -1.0628942251 #@# 4 188 -2.00660 -1.93236 -10.49993 2.00000 0.00000 4.00000 -1.0628942 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.062894 #@# 4 194 -1.62463 -1.93236 -10.49993 2.00000 0.00000 4.00000 -1.0629157 #@# 4 195 -1.68308 -1.93236 -10.49993 2.00000 0.00000 4.00000 -1.0629189 #@# 4 196 -1.73393 -1.93236 -10.49993 2.00000 0.00000 4.00000 -1.0629196 #@# 4 199 -1.77371 -1.93236 -10.49993 2.00000 0.00000 4.00000 -1.0629207 #@# 4 200 -1.79830 -1.93236 -10.49993 2.00000 0.00000 4.00000 -1.0629213 #@# 4 209 -1.79830 -1.78851 -10.49993 2.00000 0.00000 4.00000 -1.0629224 #@# 4 210 -1.79830 -1.82437 -10.49993 2.00000 0.00000 4.00000 -1.0629240 #@# 4 211 -1.79830 -1.85298 -10.49993 2.00000 0.00000 4.00000 -1.0629249 #@# 4 216 -1.79830 -1.85298 -9.49993 2.00000 0.00000 4.00000 -1.0631466 #@# 4 221 -1.79830 -1.85298 -9.43951 2.00000 0.00000 4.00000 -1.0631475 #@# 4 222 -1.79830 -1.85298 -9.42951 2.00000 0.00000 4.00000 -1.0631479 #@# 4 228 -1.79830 -1.85298 -9.42951 3.00000 0.00000 4.00000 -1.0631932 #@# 4 232 -1.79830 -1.85298 -9.42951 2.61803 0.00000 4.00000 -1.0631952 #@# 4 236 -1.79830 -1.85298 -9.42951 2.68174 0.00000 4.00000 -1.0631965 #@# 4 237 -1.79830 -1.85298 -9.42951 2.69174 0.00000 4.00000 -1.0631969 #@# 4 242 -1.79830 -1.85298 -9.42951 2.69174 -1.61803 4.00000 -1.0634632 #@# 4 243 -1.79830 -1.85298 -9.42951 2.69174 -1.60439 4.00000 -1.0634654 #@# 4 245 -1.79830 -1.85298 -9.42951 2.69174 -0.99157 4.00000 -1.0634710 #@# 4 247 -1.79830 -1.85298 -9.42951 2.69174 -1.27430 4.00000 -1.0634903 #@# 4 255 -1.79830 -1.85298 -9.42951 2.69174 -1.27430 3.38197 -1.0635272 #@# 4 257 -1.79830 -1.85298 -9.42951 2.69174 -1.27430 3.28779 -1.0635325 #@# 4 258 -1.79830 -1.85298 -9.42951 2.69174 -1.27430 3.22047 -1.0635332 #@# 4 261 -1.79830 -1.85298 -9.42951 2.69174 -1.27430 3.18831 -1.0635333 powell nthiter 1: fret = -1.063533 #@# 4 266 -0.79830 -1.85298 -9.42951 2.69174 -1.27430 3.17775 -1.0636679 #@# 4 270 -1.18026 -1.85298 -9.42951 2.69174 -1.27430 3.17775 -1.0636824 #@# 4 271 -1.05492 -1.85298 -9.42951 2.69174 -1.27430 3.17775 -1.0636853 #@# 4 275 -1.04492 -1.85298 -9.42951 2.69174 -1.27430 3.17775 -1.0636858 #@# 4 283 -1.04492 -2.14316 -9.42951 2.69174 -1.27430 3.17775 -1.0636969 #@# 4 284 -1.04492 -2.13316 -9.42951 2.69174 -1.27430 3.17775 -1.0636977 #@# 4 285 -1.04492 -2.04207 -9.42951 2.69174 -1.27430 3.17775 -1.0636981 #@# 4 290 -1.04492 -2.03153 -9.42951 2.69174 -1.27430 3.17775 -1.0636982 #@# 4 297 -1.04492 -2.03153 -9.26253 2.69174 -1.27430 3.17775 -1.0637060 #@# 4 298 -1.04492 -2.03153 -9.25253 2.69174 -1.27430 3.17775 -1.0637062 #@# 4 301 -1.04492 -2.03153 -9.21755 2.69174 -1.27430 3.17775 -1.0637063 #@# 4 309 -1.04492 -2.03153 -9.20755 3.07371 -1.27430 3.17775 -1.0637090 #@# 4 310 -1.04492 -2.03153 -9.20755 2.92259 -1.27430 3.17775 -1.0637136 #@# 4 311 -1.04492 -2.03153 -9.20755 2.90503 -1.27430 3.17775 -1.0637147 #@# 4 314 -1.04492 -2.03153 -9.20755 2.86378 -1.27430 3.17775 -1.0637153 #@# 4 318 -1.04492 -2.03153 -9.20755 2.86378 -2.89233 3.17775 -1.0637455 #@# 4 319 -1.04492 -2.03153 -9.20755 2.86378 -2.13950 3.17775 -1.0638479 #@# 4 324 -1.04492 -2.03153 -9.20755 2.86378 -2.21711 3.17775 -1.0638496 #@# 4 335 -1.04492 -2.03153 -9.20755 2.86378 -2.21711 3.55971 -1.0638520 #@# 4 336 -1.04492 -2.03153 -9.20755 2.86378 -2.21711 3.39603 -1.0638527 #@# 4 337 -1.04492 -2.03153 -9.20755 2.86378 -2.21711 3.43293 -1.0638535 #@# 4 339 -1.04492 -2.03153 -9.20755 2.86378 -2.21711 3.44293 -1.0638541 #@# 4 341 -0.29155 -2.21008 -8.98559 3.03582 -3.15991 3.70811 -1.0640959 #@# 4 344 0.92744 -2.49899 -8.62645 3.31419 -4.68541 4.13718 -1.0643787 #@# 4 347 1.67868 -2.67703 -8.40512 3.48574 -5.62554 4.40161 -1.0644164 #@# 4 350 1.77818 -2.70062 -8.37581 3.50847 -5.75006 4.43664 -1.0644168 #@# 4 352 1.73566 -2.69054 -8.38833 3.49876 -5.69685 4.42167 -1.0644188 #@# 4 353 1.72813 -2.68875 -8.39055 3.49704 -5.68742 4.41902 -1.0644193 powell nthiter 2: fret = -1.064419 #@# 4 361 1.72813 -2.68875 -8.39055 3.49704 -5.68742 4.80099 -1.0644304 #@# 4 362 1.72813 -2.68875 -8.39055 3.49704 -5.68742 4.81099 -1.0644310 #@# 4 364 1.72813 -2.68875 -8.39055 3.49704 -5.68742 4.89117 -1.0644321 #@# 4 367 1.72813 -2.68875 -8.39055 3.49704 -5.68742 4.90497 -1.0644327 #@# 4 376 1.72813 -2.69894 -8.39055 3.49704 -5.68742 4.90497 -1.0644330 #@# 4 377 1.72813 -2.71317 -8.39055 3.49704 -5.68742 4.90497 -1.0644332 #@# 4 383 1.72813 -2.71317 -9.00859 3.49704 -5.68742 4.90497 -1.0645304 #@# 4 385 1.72813 -2.71317 -9.05097 3.49704 -5.68742 4.90497 -1.0645316 #@# 4 386 1.72813 -2.71317 -9.08026 3.49704 -5.68742 4.90497 -1.0645331 #@# 4 388 1.72813 -2.71317 -9.13952 3.49704 -5.68742 4.90497 -1.0645360 #@# 4 391 1.72813 -2.71317 -9.12952 3.49704 -5.68742 4.90497 -1.0645362 #@# 4 397 1.72813 -2.71317 -9.12952 3.87900 -5.68742 4.90497 -1.0645483 #@# 4 398 1.72813 -2.71317 -9.12952 3.82685 -5.68742 4.90497 -1.0645505 #@# 4 401 1.72813 -2.71317 -9.12952 3.84677 -5.68742 4.90497 -1.0645515 #@# 4 408 1.72813 -2.71317 -9.12952 3.84677 -5.30546 4.90497 -1.0646089 #@# 4 410 1.72813 -2.71317 -9.12952 3.84677 -5.25930 4.90497 -1.0646105 #@# 4 411 1.72813 -2.71317 -9.12952 3.84677 -5.24249 4.90497 -1.0646110 #@# 4 416 2.48150 -2.89173 -8.90756 4.01881 -6.18530 5.17015 -1.0646278 #@# 4 420 2.19374 -2.82353 -8.99234 3.95310 -5.82518 5.06886 -1.0646329 powell nthiter 3: fret = -1.064633 #@# 4 433 2.20127 -2.82531 -8.99012 3.95482 -5.83461 5.06076 -1.0646333 #@# 4 453 2.20127 -2.82531 -9.04009 3.95482 -5.83461 5.06076 -1.0646348 #@# 4 473 2.20127 -2.82531 -9.04009 3.95482 -5.74550 5.06076 -1.0646390 #@# 4 475 2.20127 -2.82531 -9.04009 3.95482 -5.75550 5.06076 -1.0646392 Powell done niters total = 3 OptTimeSec 26.7 sec OptTimeMin 0.44 min nEvals 489 Final optimized parameters 2.20127034 -2.82531214 -9.04009247 3.95481586 -5.75549793 5.06076336 Final matrix parameters 2.1937 -2.8235 -9.0423 3.9531 -5.7461 5.0581 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Final cost -1.064639243547315 --------------------------------- Final RefRAS-to-MovRAS 0.99108 0.08777 -0.10028 2.20127; -0.08111 0.99434 0.06862 -2.82531; 0.10574 -0.05988 0.99259 -9.04009; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -0.02376 0.00817 -0.39921 101.15288; -0.02096 -0.39939 -0.00693 91.07527; -0.39872 0.02050 0.02415 73.69273; 0.00000 0.00000 0.00000 1.00000; Final matrix parameters 2.2013 -2.8253 -9.0401 3.9548 -5.7555 5.0608 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Final opt parameters 2.2013 -2.8253 -9.0401 3.9548 -5.7555 5.0608 nhits = 115838 out of 16777216, Percent Overlap: 44.2 mri_coreg RunTimeSec 83.3 sec To check run: tkregisterfv --mov /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii --targ /home/ward/freesurfer/subjects/original_data_both_groups/NT001_T0_MR_STRUCT/mri/brainmask.mgz --reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/mri_coreg.lta --s NT001_T0_MR_STRUCT --surfs mri_coreg done mri_segreg --mov /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii --init-reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/reg.init.dat --out-reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 7.3.2 setenv SUBJECTS_DIR /home/ward/freesurfer/subjects/original_data_both_groups cd /home/ward/freesurfer/subjects/testdtrecon mri_segreg --mov /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii --init-reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/reg.init.dat --out-reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname ward-GE72-6QD machine x86_64 user ward movvol /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii regfile /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/reg.init.dat subject NT001_T0_MR_STRUCT dof 6 outregfile /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1667557093 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.05941 0.99803 0.02043 -0.14540; 0.99686 0.06039 -0.05126 -1.56847; -0.05240 0.01732 -0.99848 29.04016; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /home/ward/freesurfer/subjects/original_data_both_groups/NT001_T0_MR_STRUCT/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.041676 1 -25.0 -25.0 25.0 1.034284 2 -25.0 25.0 -25.0 1.071962 3 -25.0 25.0 25.0 0.962662 4 25.0 -25.0 -25.0 1.063024 5 25.0 -25.0 25.0 1.046570 6 25.0 25.0 -25.0 1.023646 7 25.0 25.0 25.0 1.066014 REL: 8 0.933628 8.309838 1.038730 rel = 0.898817 Initial costs ---------------- Number of surface hits 2655 WM Intensity 19941.0208 +/- 6594.7580 Ctx Intensity 19635.4612 +/- 7704.5544 Pct Contrast -5.7373 +/- 40.9117 Cost 0.9336 RelCost 0.8988 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0278 1.0278 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9971 0.9971 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9962 0.9962 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9737 0.9737 0.0 10 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.9715 0.9715 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9710 0.9710 0.0 22 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.0000 0.9572 0.9572 0.0 24 -4.0000 -4.0000 -4.0000 4.0000 4.0000 -4.0000 0.9506 0.9506 0.0 25 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.0000 0.9416 0.9416 0.0 31 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.9362 0.9362 0.0 37 -4.0000 -4.0000 0.0000 0.0000 -4.0000 0.0000 0.9250 0.9250 0.0 117 -4.0000 0.0000 0.0000 0.0000 -4.0000 -4.0000 0.9193 0.9193 0.0 382 0.0000 0.0000 4.0000 -4.0000 0.0000 0.0000 0.9093 0.9093 0.0 Brute Force -------------------------- Min cost was 0.909268 Number of iterations 729 Search time 1.192092 sec Parameters at best (transmm, rotdeg) 0.000 0.000 4.000 -4.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 4 3 -4 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.909268 7 -0.105 0.000 4.000 -4.000 0.000 0.000 0.9079081463 8 -0.301 0.000 4.000 -4.000 0.000 0.000 0.9066365529 10 -0.242 0.000 4.000 -4.000 0.000 0.000 0.9064612986 11 -0.256 0.000 4.000 -4.000 0.000 0.000 0.9064260555 12 -0.260 0.000 4.000 -4.000 0.000 0.000 0.9064233435 13 -0.262 0.000 4.000 -4.000 0.000 0.000 0.9064225874 23 -0.261 0.050 4.000 -4.000 0.000 0.000 0.9059661138 24 -0.261 0.177 4.000 -4.000 0.000 0.000 0.9055571157 27 -0.261 0.175 4.000 -4.000 0.000 0.000 0.9055552134 30 -0.261 0.175 5.000 -4.000 0.000 0.000 0.9046973941 33 -0.261 0.175 5.618 -4.000 0.000 0.000 0.8962537534 39 -0.261 0.175 5.616 -4.000 0.000 0.000 0.8962524983 40 -0.261 0.175 5.615 -4.000 0.000 0.000 0.8962524354 48 -0.261 0.175 5.615 -3.978 0.000 0.000 0.8961132259 50 -0.261 0.175 5.615 -3.975 0.000 0.000 0.8961123582 51 -0.261 0.175 5.615 -3.976 0.000 0.000 0.8961121384 59 -0.261 0.175 5.615 -3.976 0.020 0.000 0.8959583105 60 -0.261 0.175 5.615 -3.976 0.061 0.000 0.8959483819 62 -0.261 0.175 5.615 -3.976 0.042 0.000 0.8959009894 64 -0.261 0.175 5.615 -3.976 0.044 0.000 0.8958998929 66 -0.261 0.175 5.615 -3.976 0.045 0.000 0.8958995508 76 -0.261 0.175 5.615 -3.976 0.045 -0.090 0.8958657819 78 -0.261 0.175 5.615 -3.976 0.045 -0.144 0.8950863428 81 -0.261 0.175 5.615 -3.976 0.045 -0.149 0.8950779779 83 -0.261 0.175 5.615 -3.976 0.045 -0.148 0.8950779328 powell nthiter 1: fret = 0.895078 94 -0.282 0.175 5.615 -3.976 0.045 -0.148 0.8950670782 95 -0.273 0.175 5.615 -3.976 0.045 -0.148 0.8950594596 96 -0.274 0.175 5.615 -3.976 0.045 -0.148 0.8950592863 107 -0.274 0.179 5.615 -3.976 0.045 -0.148 0.8950548154 108 -0.274 0.178 5.615 -3.976 0.045 -0.148 0.8950547480 116 -0.274 0.178 5.413 -3.976 0.045 -0.148 0.8946348131 118 -0.274 0.178 5.254 -3.976 0.045 -0.148 0.8940071373 120 -0.274 0.178 5.315 -3.976 0.045 -0.148 0.8939406958 121 -0.274 0.178 5.295 -3.976 0.045 -0.148 0.8937563379 122 -0.274 0.178 5.287 -3.976 0.045 -0.148 0.8937194836 124 -0.274 0.178 5.284 -3.976 0.045 -0.148 0.8937181599 125 -0.274 0.178 5.285 -3.976 0.045 -0.148 0.8937173178 132 -0.274 0.178 5.285 -3.965 0.045 -0.148 0.8934921105 134 -0.274 0.178 5.285 -3.924 0.045 -0.148 0.8929358074 136 -0.274 0.178 5.285 -3.916 0.045 -0.148 0.8929121133 137 -0.274 0.178 5.285 -3.915 0.045 -0.148 0.8929105512 145 -0.274 0.178 5.285 -3.915 0.236 -0.148 0.8927442746 147 -0.274 0.178 5.285 -3.915 0.309 -0.148 0.8925085506 149 -0.274 0.178 5.285 -3.915 0.281 -0.148 0.8925078498 150 -0.274 0.178 5.285 -3.915 0.295 -0.148 0.8924633256 152 -0.274 0.178 5.285 -3.915 0.294 -0.148 0.8924629098 154 -0.274 0.178 5.285 -3.915 0.293 -0.148 0.8924622555 164 -0.274 0.178 5.285 -3.915 0.293 -0.246 0.8920351695 166 -0.274 0.178 5.285 -3.915 0.293 -0.306 0.8919400125 167 -0.274 0.178 5.285 -3.915 0.293 -0.285 0.8918191985 powell nthiter 2: fret = 0.891819 185 -0.270 0.178 5.285 -3.915 0.293 -0.285 0.8918183457 186 -0.271 0.178 5.285 -3.915 0.293 -0.285 0.8918181270 194 -0.271 0.034 5.285 -3.915 0.293 -0.285 0.8916790549 195 -0.271 0.091 5.285 -3.915 0.293 -0.285 0.8903723170 196 -0.271 0.104 5.285 -3.915 0.293 -0.285 0.8901677918 198 -0.271 0.118 5.285 -3.915 0.293 -0.285 0.8901012308 199 -0.271 0.117 5.285 -3.915 0.293 -0.285 0.8901009050 200 -0.271 0.116 5.285 -3.915 0.293 -0.285 0.8901005941 211 -0.271 0.116 5.288 -3.915 0.293 -0.285 0.8900842921 213 -0.271 0.116 5.312 -3.915 0.293 -0.285 0.8899312194 215 -0.271 0.116 5.316 -3.915 0.293 -0.285 0.8899245571 216 -0.271 0.116 5.317 -3.915 0.293 -0.285 0.8899242767 226 -0.271 0.116 5.317 -3.908 0.293 -0.285 0.8898940204 227 -0.271 0.116 5.317 -3.901 0.293 -0.285 0.8898777009 229 -0.271 0.116 5.317 -3.896 0.293 -0.285 0.8898730070 230 -0.271 0.116 5.317 -3.897 0.293 -0.285 0.8898724457 238 -0.271 0.116 5.317 -3.897 0.256 -0.285 0.8895964520 241 -0.271 0.116 5.317 -3.897 0.259 -0.285 0.8895925342 243 -0.271 0.116 5.317 -3.897 0.262 -0.285 0.8895914602 254 -0.271 0.116 5.317 -3.897 0.262 -0.302 0.8894178881 256 -0.271 0.116 5.317 -3.897 0.262 -0.318 0.8893031956 258 -0.271 0.116 5.317 -3.897 0.262 -0.330 0.8892768709 267 -0.270 0.092 5.329 -3.890 0.250 -0.345 0.8892017056 268 -0.271 0.102 5.324 -3.892 0.255 -0.339 0.8891840957 269 -0.270 0.100 5.325 -3.892 0.254 -0.340 0.8891831331 270 -0.271 0.100 5.325 -3.892 0.254 -0.340 0.8891826060 powell nthiter 3: fret = 0.889183 281 -0.245 0.100 5.325 -3.892 0.254 -0.340 0.8891474553 283 -0.252 0.100 5.325 -3.892 0.254 -0.340 0.8891404346 285 -0.254 0.100 5.325 -3.892 0.254 -0.340 0.8891394873 298 -0.254 0.100 5.325 -3.892 0.254 -0.345 0.8891265679 300 -0.254 0.100 5.325 -3.892 0.254 -0.347 0.8891250405 310 -0.254 0.100 5.292 -3.892 0.254 -0.347 0.8890901988 311 -0.254 0.100 5.304 -3.892 0.254 -0.347 0.8890220389 314 -0.254 0.100 5.305 -3.892 0.254 -0.347 0.8890217639 324 -0.254 0.100 5.305 -3.901 0.254 -0.347 0.8890161375 325 -0.254 0.100 5.305 -3.899 0.254 -0.347 0.8890154997 326 -0.254 0.100 5.305 -3.898 0.254 -0.347 0.8890146670 338 -0.254 0.100 5.305 -3.898 0.252 -0.347 0.8890136198 345 -0.253 0.076 5.317 -3.891 0.241 -0.364 0.8890086893 346 -0.254 0.088 5.312 -3.895 0.246 -0.356 0.8889788155 347 -0.254 0.088 5.312 -3.895 0.246 -0.356 0.8889786868 353 -0.236 0.059 5.307 -3.893 0.230 -0.383 0.8888235050 360 -0.234 0.055 5.306 -3.892 0.228 -0.387 0.8888033486 361 -0.233 0.053 5.305 -3.892 0.227 -0.389 0.8888001341 363 -0.232 0.052 5.305 -3.892 0.226 -0.390 0.8887988028 369 -0.232 0.052 5.305 -3.892 0.226 -0.390 0.8887985321 powell nthiter 4: fret = 0.888799 378 -0.208 0.052 5.305 -3.892 0.226 -0.390 0.8887169401 379 -0.205 0.052 5.305 -3.892 0.226 -0.390 0.8887159655 390 -0.205 0.052 5.305 -3.892 0.226 -0.406 0.8886544871 392 -0.205 0.052 5.305 -3.892 0.226 -0.403 0.8886488913 403 -0.205 0.055 5.304 -3.893 0.227 -0.401 0.8886413841 404 -0.205 0.054 5.304 -3.893 0.227 -0.401 0.8886407232 416 -0.205 0.054 5.304 -3.894 0.227 -0.401 0.8886382511 417 -0.205 0.054 5.304 -3.903 0.227 -0.401 0.8886320592 419 -0.205 0.054 5.304 -3.900 0.227 -0.401 0.8886305359 431 -0.205 0.054 5.304 -3.900 0.228 -0.401 0.8886303065 440 -0.206 0.055 5.304 -3.900 0.229 -0.400 0.8886286263 441 -0.207 0.056 5.304 -3.900 0.229 -0.399 0.8886284286 442 -0.206 0.056 5.304 -3.900 0.229 -0.400 0.8886281719 445 -0.206 0.056 5.304 -3.900 0.229 -0.400 0.8886278550 powell nthiter 5: fret = 0.888628 456 -0.194 0.056 5.304 -3.900 0.229 -0.400 0.8886269688 457 -0.200 0.056 5.304 -3.900 0.229 -0.400 0.8886209767 458 -0.201 0.056 5.304 -3.900 0.229 -0.400 0.8886208996 469 -0.201 0.056 5.304 -3.900 0.229 -0.403 0.8886091457 470 -0.201 0.056 5.304 -3.900 0.229 -0.407 0.8886046514 480 -0.201 0.056 5.304 -3.900 0.229 -0.406 0.8886046108 481 -0.201 0.056 5.304 -3.900 0.229 -0.406 0.8886044673 493 -0.201 0.056 5.304 -3.903 0.229 -0.406 0.8886023741 494 -0.201 0.056 5.304 -3.904 0.229 -0.406 0.8886023349 505 -0.201 0.056 5.304 -3.904 0.231 -0.406 0.8886014607 506 -0.201 0.056 5.304 -3.904 0.232 -0.406 0.8886008221 517 -0.202 0.058 5.305 -3.905 0.233 -0.404 0.8885967642 518 -0.202 0.058 5.305 -3.905 0.233 -0.404 0.8885967134 520 -0.202 0.059 5.305 -3.905 0.233 -0.404 0.8885963359 522 -0.202 0.059 5.305 -3.905 0.233 -0.404 0.8885963259 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.091122 1 -25.0 -25.0 25.0 1.054714 2 -25.0 25.0 -25.0 1.024697 3 -25.0 25.0 25.0 1.044036 4 25.0 -25.0 -25.0 1.068893 5 25.0 -25.0 25.0 1.049095 6 25.0 25.0 -25.0 0.998442 7 25.0 25.0 25.0 1.055347 REL: 8 0.888596 8.386347 1.048293 rel = 0.84766 Number of iterations 5 Min cost was 0.888596 Number of FunctionCalls 525 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.987474 sec Parameters at optimum (transmm) -0.20246 0.05859 5.30466 Parameters at optimum (rotdeg) -3.90459 0.23319 -0.40394 Final costs ---------------- Number of surface hits 2655 WM Intensity 19239.3897 +/- 7786.8647 Ctx Intensity 19388.0562 +/- 8753.8137 Pct Contrast -2.2569 +/- 36.4571 Cost 0.8886 RelCost 0.8988 Reg at min cost was -0.05291 0.99848 0.01555 -0.22660; 0.99137 0.05439 -0.11925 0.47144; -0.11991 0.00910 -0.99274 34.38457; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/bbr.pass1.dat, type = 14 Original Reg -0.05941 0.99803 0.02043 -0.14540; 0.99686 0.06039 -0.05126 -1.56847; -0.05240 0.01732 -0.99848 29.04016; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00650 -0.00045 0.00488 0.08120; 0.00548 0.00600 0.06799 -2.03991; 0.06752 0.00821 -0.00573 -5.34441; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 7.843388 Computing change in rh position Surface-RMS-Diff-mm 6.049859 2.156838 10.493069 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii --init-reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/bbr.pass1.dat --out-reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/ward/freesurfer/subjects/testdtrecon/dti/register.dat.mincost --dof 6 --nmax 36 --param /home/ward/freesurfer/subjects/testdtrecon/dti/register.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.3.2 setenv SUBJECTS_DIR /home/ward/freesurfer/subjects/original_data_both_groups cd /home/ward/freesurfer/subjects/testdtrecon mri_segreg --mov /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii --init-reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/bbr.pass1.dat --out-reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/ward/freesurfer/subjects/testdtrecon/dti/register.dat.mincost --dof 6 --nmax 36 --param /home/ward/freesurfer/subjects/testdtrecon/dti/register.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname ward-GE72-6QD machine x86_64 user ward movvol /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/template.nii regfile /home/ward/freesurfer/subjects/testdtrecon/dti/tmp.bbregister.31299/bbr.pass1.dat subject NT001_T0_MR_STRUCT dof 6 outregfile /home/ward/freesurfer/subjects/testdtrecon/dti/register.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1667004784 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.05291 0.99848 0.01555 -0.22660; 0.99137 0.05439 -0.11925 0.47144; -0.11991 0.00910 -0.99274 34.38457; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /home/ward/freesurfer/subjects/original_data_both_groups/NT001_T0_MR_STRUCT/mri/orig.mgz Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 1.050800 1 -25.0 -25.0 25.0 1.039296 2 -25.0 25.0 -25.0 1.047935 3 -25.0 25.0 25.0 1.020536 4 25.0 -25.0 -25.0 1.039917 5 25.0 -25.0 25.0 1.044055 6 25.0 25.0 -25.0 1.031206 7 25.0 25.0 25.0 1.036601 REL: 8 0.939605 8.310346 1.038793 rel = 0.904516 Initial costs ---------------- Number of surface hits 265721 WM Intensity 19256.3884 +/- 7710.9653 Ctx Intensity 19229.3928 +/- 8346.5363 Pct Contrast -2.6366 +/- 35.5767 Cost 0.9396 RelCost 0.9045 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.8928 0.8928 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.8910 0.8910 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.8883 0.8883 0.0 249 0.0000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.8872 0.8872 0.0 258 0.0000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.8870 0.8870 0.0 Brute Force -------------------------- Min cost was 0.887027 Number of iterations 729 Search time 1.164352 sec Parameters at best (transmm, rotdeg) 0.000 -0.100 -0.100 0.000 0.100 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -0.1 2 -0.1 3 0 4 0.1 5 -0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.939638 2 1.000 -0.100 -0.100 0.000 0.100 -0.100 0.9384634145 6 0.618 -0.100 -0.100 0.000 0.100 -0.100 0.9372508405 8 0.622 -0.100 -0.100 0.000 0.100 -0.100 0.9372446667 10 0.672 -0.100 -0.100 0.000 0.100 -0.100 0.9372095164 11 0.670 -0.100 -0.100 0.000 0.100 -0.100 0.9372086530 12 0.662 -0.100 -0.100 0.000 0.100 -0.100 0.9372079774 14 0.665 -0.100 -0.100 0.000 0.100 -0.100 0.9372075131 15 0.666 -0.100 -0.100 0.000 0.100 -0.100 0.9372075064 18 0.666 0.900 -0.100 0.000 0.100 -0.100 0.9313814209 21 0.666 1.518 -0.100 0.000 0.100 -0.100 0.9295339996 23 0.666 1.480 -0.100 0.000 0.100 -0.100 0.9295294301 24 0.666 1.488 -0.100 0.000 0.100 -0.100 0.9295255476 25 0.666 1.496 -0.100 0.000 0.100 -0.100 0.9295240027 26 0.666 1.499 -0.100 0.000 0.100 -0.100 0.9295236321 29 0.666 1.502 -0.100 0.000 0.100 -0.100 0.9295236005 31 0.666 1.501 -0.100 0.000 0.100 -0.100 0.9295234840 34 0.666 1.501 -1.718 0.000 0.100 -0.100 0.9286738437 35 0.666 1.501 -0.989 0.000 0.100 -0.100 0.9286661860 39 0.666 1.501 -1.101 0.000 0.100 -0.100 0.9286470403 40 0.666 1.501 -1.117 0.000 0.100 -0.100 0.9286326267 41 0.666 1.501 -1.175 0.000 0.100 -0.100 0.9286261796 42 0.666 1.501 -1.151 0.000 0.100 -0.100 0.9286179894 43 0.666 1.501 -1.150 0.000 0.100 -0.100 0.9286177007 44 0.666 1.501 -1.138 0.000 0.100 -0.100 0.9286150631 48 0.666 1.501 -1.139 0.000 0.100 -0.100 0.9286149697 51 0.666 1.501 -1.139 1.000 0.100 -0.100 0.9226475437 52 0.666 1.501 -1.139 2.618 0.100 -0.100 0.9204235108 57 0.666 1.501 -1.139 2.000 0.100 -0.100 0.9203663347 63 0.666 1.501 -1.139 1.961 0.100 -0.100 0.9203509048 64 0.666 1.501 -1.139 1.954 0.100 -0.100 0.9203508322 65 0.666 1.501 -1.139 1.957 0.100 -0.100 0.9203505890 74 0.666 1.501 -1.139 1.958 0.160 -0.100 0.9203484108 75 0.666 1.501 -1.139 1.958 0.133 -0.100 0.9203421970 76 0.666 1.501 -1.139 1.958 0.132 -0.100 0.9203420810 77 0.666 1.501 -1.139 1.958 0.119 -0.100 0.9203396234 79 0.666 1.501 -1.139 1.958 0.116 -0.100 0.9203392756 87 0.666 1.501 -1.139 1.958 0.116 0.282 0.9199313568 91 0.666 1.501 -1.139 1.958 0.116 0.274 0.9199310238 92 0.666 1.501 -1.139 1.958 0.116 0.277 0.9199306335 95 1.331 3.102 -2.178 3.916 0.133 0.656 0.9045010938 102 1.277 2.972 -2.093 3.757 0.132 0.625 0.9038457116 104 1.282 2.983 -2.101 3.771 0.132 0.628 0.9038236491 105 1.301 3.028 -2.130 3.826 0.132 0.639 0.9037803215 107 1.294 3.012 -2.120 3.807 0.132 0.635 0.9037475028 108 1.289 3.001 -2.113 3.793 0.132 0.632 0.9037304413 110 1.291 3.004 -2.115 3.797 0.132 0.633 0.9037273640 powell nthiter 1: fret = 0.903727 113 2.291 3.004 -2.115 3.797 0.132 0.633 0.9010300712 117 1.909 3.004 -2.115 3.797 0.132 0.633 0.9004434733 119 1.936 3.004 -2.115 3.797 0.132 0.633 0.9004364089 121 1.929 3.004 -2.115 3.797 0.132 0.633 0.9004351140 122 1.928 3.004 -2.115 3.797 0.132 0.633 0.9004350278 123 1.926 3.004 -2.115 3.797 0.132 0.633 0.9004350200 130 1.926 2.386 -2.115 3.797 0.132 0.633 0.9000220873 132 1.926 2.624 -2.115 3.797 0.132 0.633 0.8997508056 133 1.926 2.625 -2.115 3.797 0.132 0.633 0.8997494502 135 1.926 2.696 -2.115 3.797 0.132 0.633 0.8997196832 136 1.926 2.678 -2.115 3.797 0.132 0.633 0.8997093651 138 1.926 2.680 -2.115 3.797 0.132 0.633 0.8997089268 139 1.926 2.686 -2.115 3.797 0.132 0.633 0.8997080761 148 1.926 2.686 -1.733 3.797 0.132 0.633 0.8992862203 149 1.926 2.686 -1.825 3.797 0.132 0.633 0.8991366804 150 1.926 2.686 -1.865 3.797 0.132 0.633 0.8990693751 151 1.926 2.686 -1.960 3.797 0.132 0.633 0.8990250112 152 1.926 2.686 -1.938 3.797 0.132 0.633 0.8990230679 153 1.926 2.686 -1.943 3.797 0.132 0.633 0.8990221049 154 1.926 2.686 -1.946 3.797 0.132 0.633 0.8990215271 155 1.926 2.686 -1.951 3.797 0.132 0.633 0.8990206580 170 1.926 2.686 -1.952 3.797 0.132 0.635 0.8990203082 174 1.926 2.686 -1.952 3.797 1.132 0.635 0.8925715959 181 1.926 2.686 -1.952 3.797 1.144 0.635 0.8925683028 182 1.926 2.686 -1.952 3.797 1.154 0.635 0.8925652578 184 1.926 2.686 -1.952 3.797 1.185 0.635 0.8925611066 185 1.926 2.686 -1.952 3.797 1.184 0.635 0.8925610760 195 1.937 2.713 -1.970 3.830 1.184 0.641 0.8925349874 196 1.938 2.715 -1.971 3.832 1.184 0.642 0.8925313421 197 1.944 2.731 -1.982 3.852 1.184 0.645 0.8925061156 199 1.943 2.728 -1.980 3.848 1.184 0.645 0.8925046154 powell nthiter 2: fret = 0.892505 203 2.943 2.728 -1.980 3.848 1.184 0.645 0.8896272946 207 2.561 2.728 -1.980 3.848 1.184 0.645 0.8886105569 208 2.606 2.728 -1.980 3.848 1.184 0.645 0.8885878548 209 2.611 2.728 -1.980 3.848 1.184 0.645 0.8885860622 212 2.625 2.728 -1.980 3.848 1.184 0.645 0.8885805364 214 2.630 2.728 -1.980 3.848 1.184 0.645 0.8885797562 230 2.631 2.726 -1.980 3.848 1.184 0.645 0.8885788074 231 2.631 2.725 -1.980 3.848 1.184 0.645 0.8885787431 239 2.631 2.725 -1.914 3.848 1.184 0.645 0.8884844186 240 2.631 2.725 -1.884 3.848 1.184 0.645 0.8884778699 242 2.631 2.725 -1.879 3.848 1.184 0.645 0.8884774196 255 2.631 2.725 -1.880 3.848 1.184 0.453 0.8881954497 258 2.631 2.725 -1.880 3.848 1.184 0.469 0.8881851380 260 2.631 2.725 -1.880 3.848 1.184 0.470 0.8881849860 268 2.631 2.725 -1.880 3.848 1.322 0.470 0.8880206660 272 2.631 2.725 -1.880 3.848 1.323 0.470 0.8880206571 284 2.624 2.707 -1.868 3.826 1.322 0.466 0.8879601105 286 2.625 2.709 -1.870 3.829 1.322 0.466 0.8879599757 294 2.885 2.702 -1.828 3.822 1.375 0.398 0.8876235598 295 2.865 2.703 -1.831 3.823 1.371 0.404 0.8876049198 296 2.825 2.704 -1.838 3.824 1.363 0.414 0.8875595140 299 2.824 2.704 -1.838 3.824 1.363 0.414 0.8875593006 301 2.823 2.704 -1.838 3.824 1.363 0.415 0.8875592145 powell nthiter 3: fret = 0.887559 312 2.793 2.633 -1.793 3.738 1.362 0.398 0.8874882486 314 2.803 2.657 -1.808 3.767 1.362 0.404 0.8874688187 317 2.806 2.664 -1.812 3.775 1.362 0.405 0.8874682292 318 2.804 2.661 -1.811 3.772 1.362 0.405 0.8874680450 326 2.804 2.518 -1.811 3.772 1.362 0.405 0.8872120795 327 2.804 2.498 -1.811 3.772 1.362 0.405 0.8871745839 329 2.804 2.456 -1.811 3.772 1.362 0.405 0.8870856039 331 2.804 2.448 -1.811 3.772 1.362 0.405 0.8870818953 340 2.804 2.448 -1.981 3.772 1.362 0.405 0.8869604576 344 2.804 2.448 -2.041 3.772 1.362 0.405 0.8868645759 347 2.804 2.448 -2.039 3.772 1.362 0.405 0.8868642622 355 2.804 2.448 -2.039 3.772 1.362 0.282 0.8868047224 356 2.804 2.448 -2.039 3.772 1.362 0.312 0.8867759790 365 2.804 2.448 -2.039 3.772 1.744 0.312 0.8867317381 366 2.804 2.448 -2.039 3.772 1.558 0.312 0.8861792708 368 2.804 2.448 -2.039 3.772 1.564 0.312 0.8861779252 371 2.804 2.448 -2.039 3.772 1.574 0.312 0.8861774173 374 2.804 2.448 -2.039 3.772 1.572 0.312 0.8861773166 381 2.796 2.448 -2.041 3.772 1.571 0.314 0.8861712813 384 2.790 2.448 -2.041 3.772 1.569 0.316 0.8861709208 385 2.791 2.448 -2.041 3.772 1.570 0.316 0.8861707286 386 2.792 2.448 -2.041 3.772 1.570 0.315 0.8861706798 powell nthiter 4: fret = 0.886171 397 2.793 2.450 -2.042 3.774 1.570 0.316 0.8861698646 409 2.793 2.451 -2.042 3.774 1.570 0.316 0.8861698587 419 2.793 2.451 -2.058 3.774 1.570 0.316 0.8861681252 422 2.793 2.451 -2.075 3.774 1.570 0.316 0.8861616473 425 2.793 2.451 -2.074 3.774 1.570 0.316 0.8861616194 436 2.793 2.451 -2.073 3.774 1.570 0.306 0.8861541420 437 2.793 2.451 -2.073 3.774 1.570 0.303 0.8861534894 439 2.793 2.451 -2.073 3.774 1.570 0.304 0.8861533366 448 2.793 2.451 -2.073 3.774 1.590 0.304 0.8861374533 450 2.793 2.451 -2.073 3.774 1.592 0.304 0.8861365971 451 2.793 2.451 -2.073 3.774 1.594 0.304 0.8861363267 459 2.798 2.451 -2.072 3.774 1.595 0.302 0.8861363025 460 2.796 2.451 -2.072 3.774 1.594 0.303 0.8861361508 461 2.795 2.451 -2.073 3.774 1.594 0.303 0.8861360795 powell nthiter 5: fret = 0.886136 484 2.795 2.452 -2.073 3.774 1.594 0.303 0.8861356199 496 2.795 2.452 -2.074 3.774 1.594 0.303 0.8861355385 506 2.795 2.452 -2.074 3.774 1.594 0.304 0.8861354901 518 2.795 2.452 -2.074 3.774 1.592 0.304 0.8861354165 520 2.795 2.452 -2.074 3.774 1.593 0.304 0.8861353813 527 2.797 2.452 -2.074 3.774 1.594 0.304 0.8861350717 529 2.798 2.452 -2.074 3.774 1.594 0.304 0.8861350170 powell nthiter 6: fret = 0.886135 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 1.044058 1 -25.0 -25.0 25.0 1.054141 2 -25.0 25.0 -25.0 1.039322 3 -25.0 25.0 25.0 1.011152 4 25.0 -25.0 -25.0 1.051166 5 25.0 -25.0 25.0 1.066425 6 25.0 25.0 -25.0 1.029724 7 25.0 25.0 25.0 1.029200 REL: 8 0.886135 8.325187 1.040648 rel = 0.851522 Number of iterations 6 Min cost was 0.886135 Number of FunctionCalls 598 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 33.848392 sec Parameters at optimum (transmm) 2.79855 2.45160 -2.07349 Parameters at optimum (rotdeg) 3.77382 1.59395 0.30362 Final costs ---------------- Number of surface hits 265721 WM Intensity 19512.4872 +/- 7321.8418 Ctx Intensity 19765.9890 +/- 7894.5556 Pct Contrast -1.0821 +/- 33.8682 Cost 0.8861 RelCost 0.9045 Reg at min cost was -0.05968 0.99815 -0.01195 3.53676; 0.99681 0.05896 -0.05371 0.66279; -0.05291 -0.01512 -0.99848 32.26056; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /home/ward/freesurfer/subjects/testdtrecon/dti/register.dat, type = 14 Original Reg -0.05291 0.99848 0.01555 -0.22660; 0.99137 0.05439 -0.11925 0.47144; -0.11991 0.00910 -0.99274 34.38457; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00678 0.00033 0.02749 -3.76336; -0.00544 -0.00457 -0.06553 -0.19134; -0.06700 0.02422 0.00574 2.12400; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 5.906792 Computing change in rh position Surface-RMS-Diff-mm 5.271337 1.230716 8.075831 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done MinCost: 0.886135 19512.487161 19765.988971 -1.082125 tkregister2_cmdl --mov /home/ward/freesurfer/subjects/testdtrecon/dti/lowb.nii.gz --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.dat --noedit --ltaout /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/ward/freesurfer/subjects/testdtrecon/dti/lowb.nii.gz reg file /home/ward/freesurfer/subjects/testdtrecon/dti/register.dat LoadVol 0 ZeroCRAS 0 7.3.2 Diagnostic Level -1 ---- Input registration matrix -------- -0.05968 0.99815 -0.01195 3.53676; 0.99681 0.05896 -0.05371 0.66279; -0.05291 -0.01512 -0.99848 32.26056; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /home/ward/freesurfer/subjects/original_data_both_groups/NT001_T0_MR_STRUCT/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /home/ward/freesurfer/subjects/testdtrecon/dti/lowb.nii.gz Tmov: -------------------- -2.50000 0.00000 0.00000 120.00000; 0.00000 0.00000 2.50013 -72.50388; 0.00000 -2.50000 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.05968 0.99815 -0.01195 3.53676; 0.99681 0.05896 -0.05371 0.66279; -0.05291 -0.01512 -0.99848 32.26056; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = NT001_T0_MR_STRUCT RegMat --------------------------- -0.05968 0.99815 -0.01195 3.53676; 0.99681 0.05896 -0.05371 0.66279; -0.05291 -0.01512 -0.99848 32.26056; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at wo 26 okt 2022 11:10:35 CEST Ended at wo 26 okt 2022 11:12:45 CEST BBR-Run-Time-Sec 130 bbregister Done To check results, run: tkregisterfv --mov /home/ward/freesurfer/subjects/testdtrecon/dti/lowb.nii.gz --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --surfs --sd /home/ward/freesurfer/subjects/original_data_both_groups #@#------------------------------- Reslicing to Tal wo 26 okt 2022 11:12:45 CEST cd /home/ward/freesurfer/subjects/testdtrecon mri_vol2vol --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --tal --interp nearest --mov /home/ward/freesurfer/subjects/testdtrecon/dti/mask.nii.gz --o /home/ward/freesurfer/subjects/testdtrecon/dti/mask-tal.nii.gz regio_read_register: loading lta Matrix from regfile: -0.05968 0.99815 -0.01195 3.53677; 0.99681 0.05896 -0.05371 0.66278; -0.05291 -0.01512 -0.99848 32.26054; 0.00000 0.00000 0.00000 1.00000; movvol /home/ward/freesurfer/subjects/testdtrecon/dti/mask.nii.gz targvol /home/ward/freesurfer/average/mni305.cor.subfov2.mgz outvol /home/ward/freesurfer/subjects/testdtrecon/dti/mask-tal.nii.gz regfile /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1667362450 Compute R for talairach space matrix from regfile ---------------------- -0.05968 0.99815 -0.01195 3.53677; 0.99681 0.05896 -0.05371 0.66278; -0.05291 -0.01512 -0.99848 32.26054; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.09008 0.07673 -0.02898 1.11987; -0.09128 1.04593 0.07877 -10.38096; 0.03217 0.00886 1.08450 -36.05749; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.02740 0.95298 -0.07950 -5.48555; 0.91428 -0.01049 -0.02434 -3.22741; -0.02178 -0.00506 -0.92091 -9.13679; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.02192 -0.06360 -0.76238 87.22886; -0.01743 -0.73672 0.00405 80.12434; -0.73138 0.01947 -0.00839 55.15199; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done cd /home/ward/freesurfer/subjects/testdtrecon mri_vol2vol --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --tal --mov /home/ward/freesurfer/subjects/testdtrecon/dti/fa.nii.gz --o /home/ward/freesurfer/subjects/testdtrecon/dti/fa-tal.nii.gz regio_read_register: loading lta Matrix from regfile: -0.05968 0.99815 -0.01195 3.53677; 0.99681 0.05896 -0.05371 0.66278; -0.05291 -0.01512 -0.99848 32.26054; 0.00000 0.00000 0.00000 1.00000; movvol /home/ward/freesurfer/subjects/testdtrecon/dti/fa.nii.gz targvol /home/ward/freesurfer/average/mni305.cor.subfov2.mgz outvol /home/ward/freesurfer/subjects/testdtrecon/dti/fa-tal.nii.gz regfile /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1667476238 Compute R for talairach space matrix from regfile ---------------------- -0.05968 0.99815 -0.01195 3.53677; 0.99681 0.05896 -0.05371 0.66278; -0.05291 -0.01512 -0.99848 32.26054; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.09008 0.07673 -0.02898 1.11987; -0.09128 1.04593 0.07877 -10.38096; 0.03217 0.00886 1.08450 -36.05749; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.02740 0.95298 -0.07950 -5.48555; 0.91428 -0.01049 -0.02434 -3.22741; -0.02178 -0.00506 -0.92091 -9.13679; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.02192 -0.06360 -0.76238 87.22886; -0.01743 -0.73672 0.00405 80.12434; -0.73138 0.01947 -0.00839 55.15199; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done dt_recon finished without error at wo 26 okt 2022 11:12:45 CEST echo "" | tee -a $LF echo tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log endif endif else else if ( $DoTalairach ) then if ( 1 ) then echo "#@#-------------------------------" | tee -a $LF echo #@#------------------------------- tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log #@#------------------------------- echo "Reslicing to Tal" | tee -a $LF echo Reslicing to Tal tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log Reslicing to Tal if ( ! -e $reg ) then if ( ! -e /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta ) then date | tee -a $LF date tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log wo 26 okt 2022 11:12:45 CEST set mask = $OutDir/mask.nii.gz set mask = /home/ward/freesurfer/subjects/testdtrecon/dti/mask.nii.gz set masktal = $OutDir/mask-tal.nii.gz set masktal = /home/ward/freesurfer/subjects/testdtrecon/dti/mask-tal.nii.gz set cmd = ( mri_vol2vol --reg $reg --tal --interp nearest --mov $mask --o $masktal ) set cmd = ( mri_vol2vol --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --tal --interp nearest --mov /home/ward/freesurfer/subjects/testdtrecon/dti/mask.nii.gz --o /home/ward/freesurfer/subjects/testdtrecon/dti/mask-tal.nii.gz ) echo "cd `pwd`" | tee -a $LF echo cd `pwd` tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log pwd cd /home/ward/freesurfer/subjects/testdtrecon echo $cmd | tee -a $LF tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log echo mri_vol2vol --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --tal --interp nearest --mov /home/ward/freesurfer/subjects/testdtrecon/dti/mask.nii.gz --o /home/ward/freesurfer/subjects/testdtrecon/dti/mask-tal.nii.gz mri_vol2vol --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --tal --interp nearest --mov /home/ward/freesurfer/subjects/testdtrecon/dti/mask.nii.gz --o /home/ward/freesurfer/subjects/testdtrecon/dti/mask-tal.nii.gz $cmd | & tee -a $LF tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log mri_vol2vol --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --tal --interp nearest --mov /home/ward/freesurfer/subjects/testdtrecon/dti/mask.nii.gz --o /home/ward/freesurfer/subjects/testdtrecon/dti/mask-tal.nii.gz regio_read_register: loading lta Matrix from regfile: -0.05968 0.99815 -0.01195 3.53677; 0.99681 0.05896 -0.05371 0.66278; -0.05291 -0.01512 -0.99848 32.26054; 0.00000 0.00000 0.00000 1.00000; movvol /home/ward/freesurfer/subjects/testdtrecon/dti/mask.nii.gz targvol /home/ward/freesurfer/average/mni305.cor.subfov2.mgz outvol /home/ward/freesurfer/subjects/testdtrecon/dti/mask-tal.nii.gz regfile /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta invert 0 tal 1 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1667362450 Compute R for talairach space matrix from regfile ---------------------- -0.05968 0.99815 -0.01195 3.53677; 0.99681 0.05896 -0.05371 0.66278; -0.05291 -0.01512 -0.99848 32.26054; 0.00000 0.00000 0.00000 1.00000; Xtal ---------------------- 1.09008 0.07673 -0.02898 1.11987; -0.09128 1.04593 0.07877 -10.38096; 0.03217 0.00886 1.08450 -36.05749; 0.00000 0.00000 0.00000 1.00000; Rtal ---------------------- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; Final tkRAS-to-tkRAS Matrix is: 0.02740 0.95298 -0.07950 -5.48555; 0.91428 -0.01049 -0.02434 -3.22741; -0.02178 -0.00506 -0.92091 -9.13679; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 0.02192 -0.06360 -0.76238 87.22886; -0.01743 -0.73672 0.00405 80.12434; -0.73138 0.01947 -0.00839 55.15199; 0.00000 0.00000 0.00000 1.00000; Resampling mri_vol2vol done if ( $status ) exit 1 ; if ( 0 ) exit 1 echo "" | tee -a $LF echo tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log echo "" | tee -a $LF echo tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log set fa = $OutDir/fa.nii.gz set fa = /home/ward/freesurfer/subjects/testdtrecon/dti/fa.nii.gz set fatal = $OutDir/fa-tal.nii.gz set fatal = /home/ward/freesurfer/subjects/testdtrecon/dti/fa-tal.nii.gz set cmd = ( mri_vol2vol --reg $reg --tal --mov $fa --o $fatal ) set cmd = ( mri_vol2vol --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --tal --mov /home/ward/freesurfer/subjects/testdtrecon/dti/fa.nii.gz --o /home/ward/freesurfer/subjects/testdtrecon/dti/fa-tal.nii.gz ) echo "cd `pwd`" | tee -a $LF echo cd `pwd` tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log pwd cd /home/ward/freesurfer/subjects/testdtrecon echo $cmd | tee -a $LF echo mri_vol2vol --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --tal --mov /home/ward/freesurfer/subjects/testdtrecon/dti/fa.nii.gz --o /home/ward/freesurfer/subjects/testdtrecon/dti/fa-tal.nii.gz tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log mri_vol2vol --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --tal --mov /home/ward/freesurfer/subjects/testdtrecon/dti/fa.nii.gz --o /home/ward/freesurfer/subjects/testdtrecon/dti/fa-tal.nii.gz $cmd | & tee -a $LF tee -a /home/ward/freesurfer/subjects/testdtrecon/dti/dt_recon.log mri_vol2vol --reg /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta --tal --mov /home/ward/freesurfer/subjects/testdtrecon/dti/fa.nii.gz --o /home/ward/freesurfer/subjects/testdtrecon/dti/fa-tal.nii.gz regio_read_register: loading lta Matrix from regfile: -0.05968 0.99815 -0.01195 3.53677; 0.99681 0.05896 -0.05371 0.66278; -0.05291 -0.01512 -0.99848 32.26054; 0.00000 0.00000 0.00000 1.00000; movvol /home/ward/freesurfer/subjects/testdtrecon/dti/fa.nii.gz targvol /home/ward/freesurfer/average/mni305.cor.subfov2.mgz outvol /home/ward/freesurfer/subjects/testdtrecon/dti/fa-tal.nii.gz regfile /home/ward/freesurfer/subjects/testdtrecon/dti/register.lta