External Email - Use Caution Hi All,
I'm running FS v. 5.3 on Gentoo Linux. I made a study, where all subjects during one session had T1, resting-state and task-based fMRI. I processed all anatomical data through standard recon-all (it worked well), and the task-based fMRI through FS-FAST - which also generated fine results. Now I wanted to look into the rs-fMRI with functional connectivity. I made a separate directory tree for this purpose (in order not to mess task and rest data), and unfortunately the bbregister doesn't handle the registration during preproc-sess properly. Misalignment is big and covers all runs. BBR-sums of all of participants (N=39) exceed 0.8 (some of them exceed 1.0). What's interesting is that bbregister previously managed the task-based fMRI data well (with no BBR-sum exceeding 0.8). I double checked the data for any i.e. conversion/orientation faults, but found none. The command for preprocessing was identical in rs-fMRI and task-based fMRI: preproc-sess -sf <sessid> -d <ProjectDirectory> -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -fsd bold I attach exemplary register log file from rs-fMRI subject registration (BBRsum=0.9704). This subject's task-based fMRI BBR-sum was 0.55. My question is - what may be the cause of such a discrepancy between registration of two functional runs taken one by one (the rs-fMRI preceded the task based)? Does anyone have an idea how to fix the problem? Best regards, Patrycja
Logfile for bbregister Sat May 12 13:11:31 CEST 2018 setenv SUBJECTS_DIR /home/pati/Freesurfer/subjects cd /home/pati/Freesurfer/NCN_rest/Neuro_rest_ST/Sub_001 /usr/local/freesurfer/bin/bbregister --s Sub_001 --init-fsl --6 --bold --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --init-reg-out bold/001/init.register.dof6.dat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux luria 4.4.6-gentoo #8 SMP Sun Aug 14 13:05:27 CEST 2016 x86_64 Intel(R) Core(TM) i7-4600U CPU @ 2.10GHz GenuineIntel GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert bold/001/template.nii.gz bold/001/tmp.bbregister.4942/template.nii mri_convert bold/001/template.nii.gz bold/001/tmp.bbregister.4942/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from bold/001/template.nii.gz... TR=1500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99912, -0.0179349, -0.0379071) j_ras = (-0.0158656, 0.998404, -0.0542015) k_ras = (-0.0388187, 0.0535524, 0.99781) writing to bold/001/tmp.bbregister.4942/template.nii... fslregister --s Sub_001 --mov bold/001/tmp.bbregister.4942/template.nii --reg bold/001/tmp.bbregister.4942/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/001/tmp.bbregister.4942/fslregister --dof 6 --fsvol brainmask.mgz Log file is bold/001/tmp.bbregister.4942/reg.init.dat.fslregister.log Sat May 12 13:11:31 CEST 2018 --s Sub_001 --mov bold/001/tmp.bbregister.4942/template.nii --reg bold/001/tmp.bbregister.4942/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/001/tmp.bbregister.4942/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ luria Linux luria 4.4.6-gentoo #8 SMP Sun Aug 14 13:05:27 CEST 2016 x86_64 Intel(R) Core(TM) i7-4600U CPU @ 2.10GHz GenuineIntel GNU/Linux nIters 1 -------------------------------------- /home/pati/Freesurfer/NCN_rest/Neuro_rest_ST/Sub_001 mri_convert /home/pati/Freesurfer/subjects/Sub_001/mri/brainmask.mgz bold/001/tmp.bbregister.4942/fslregister/refvol.fslregister.nii mri_convert /home/pati/Freesurfer/subjects/Sub_001/mri/brainmask.mgz bold/001/tmp.bbregister.4942/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/pati/Freesurfer/subjects/Sub_001/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.32831e-10, 0) j_ras = (-3.72529e-09, -7.45058e-09, -1) k_ras = (4.65661e-10, 1, 7.45058e-09) writing to bold/001/tmp.bbregister.4942/fslregister/refvol.fslregister.nii... -------------------------------------- /home/pati/Freesurfer/NCN_rest/Neuro_rest_ST/Sub_001 mri_convert bold/001/tmp.bbregister.4942/template.nii bold/001/tmp.bbregister.4942/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/001/tmp.bbregister.4942/template.nii bold/001/tmp.bbregister.4942/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from bold/001/tmp.bbregister.4942/template.nii... TR=1500.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99912, -0.0179349, -0.0379071) j_ras = (-0.0158656, 0.998404, -0.0542015) k_ras = (-0.0388187, 0.0535524, 0.99781) keeping frame 0 writing to bold/001/tmp.bbregister.4942/fslregister/movvol.fslregister.nii... Mov determinant is -38.9924 /home/pati/Freesurfer/NCN_rest/Neuro_rest_ST/Sub_001 tkregister2_cmdl --mov bold/001/tmp.bbregister.4942/fslregister/movvol.fslregister.nii --reg bold/001/tmp.bbregister.4942/fslregister/reg0.4977.dat --regheader --fslregout bold/001/tmp.bbregister.4942/reg.init.dat.fsl.mat0 --s Sub_001 --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/001/tmp.bbregister.4942/fslregister/movvol.fslregister.nii reg file bold/001/tmp.bbregister.4942/fslregister/reg0.4977.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/pati/Freesurfer/subjects/Sub_001/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 bold/001/tmp.bbregister.4942/fslregister/movvol.fslregister.nii Tmov: -------------------- -3.438 0.000 0.000 110.000; 0.000 0.000 3.300 -57.747; 0.000 -3.438 0.000 110.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.999 0.018 0.038 2.494; -0.039 0.054 0.998 -11.832; 0.016 -0.998 0.054 -4.394; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 0.018 0.038 2.494; -0.039 0.054 0.998 -11.832; 0.016 -0.998 0.054 -4.394; 0.000 0.000 0.000 1.000; Determinant 1 subject = Sub_001 RegMat --------------------------- 0.999 0.018 0.038 2.494; -0.039 0.054 0.998 -11.832; 0.016 -0.998 0.054 -4.394; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -38.9924, ref det = -1 Sat May 12 13:11:32 CEST 2018 /home/pati/Freesurfer/NCN_rest/Neuro_rest_ST/Sub_001 flirt.fsl -ref bold/001/tmp.bbregister.4942/fslregister/refvol.fslregister.nii -in bold/001/tmp.bbregister.4942/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/001/tmp.bbregister.4942/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init bold/001/tmp.bbregister.4942/reg.init.dat.fsl.mat0 Sat May 12 13:11:37 CEST 2018 /home/pati/Freesurfer/NCN_rest/Neuro_rest_ST/Sub_001 flirt.fsl -ref bold/001/tmp.bbregister.4942/fslregister/refvol.fslregister.nii -in bold/001/tmp.bbregister.4942/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/001/tmp.bbregister.4942/reg.init.dat.fsl.mat -init bold/001/tmp.bbregister.4942/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Sub_001 --mov bold/001/tmp.bbregister.4942/template.nii --reg bold/001/tmp.bbregister.4942/reg.init.dat --fslreg bold/001/tmp.bbregister.4942/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.999 0.019 0.043 16.240; 0.042 0.028 -0.999 174.497; -0.020 0.999 0.027 16.574; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/001/tmp.bbregister.4942/template.nii reg file bold/001/tmp.bbregister.4942/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/pati/Freesurfer/subjects/Sub_001/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 bold/001/tmp.bbregister.4942/template.nii Tmov: -------------------- -3.438 0.000 0.000 110.000; 0.000 0.000 3.300 -57.747; 0.000 -3.438 0.000 110.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -38.9924, ref det = -1 ---- Input registration matrix (computed) -------- 0.999 0.020 0.042 2.592; -0.043 0.027 0.999 -3.507; 0.019 -0.999 0.028 -2.203; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 0.020 0.042 2.592; -0.043 0.027 0.999 -3.507; 0.019 -0.999 0.028 -2.203; 0.000 0.000 0.000 1.000; Determinant 1 subject = Sub_001 RegMat --------------------------- 0.999 0.020 0.042 2.592; -0.043 0.027 0.999 -3.507; 0.019 -0.999 0.028 -2.203; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: S Started at Sat May 12 13:11:31 CEST 2018 Ended at Sat May 12 13:11:47 CEST 2018 fslregister Done To check results, run: tkregister2 --mov bold/001/tmp.bbregister.4942/template.nii --reg bold/001/tmp.bbregister.4942/reg.init.dat --surf orig mri_segreg --mov bold/001/tmp.bbregister.4942/template.nii --init-reg bold/001/tmp.bbregister.4942/reg.init.dat --out-reg bold/001/tmp.bbregister.4942/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 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /home/pati/Freesurfer/subjects cd /home/pati/Freesurfer/NCN_rest/Neuro_rest_ST/Sub_001 mri_segreg --mov bold/001/tmp.bbregister.4942/template.nii --init-reg bold/001/tmp.bbregister.4942/reg.init.dat --out-reg bold/001/tmp.bbregister.4942/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 luria machine x86_64 user pati movvol bold/001/tmp.bbregister.4942/template.nii regfile bold/001/tmp.bbregister.4942/reg.init.dat subject Sub_001 dof 6 outregfile bold/001/tmp.bbregister.4942/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 1526875627 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 0.020 0.042 2.592; -0.043 0.027 0.999 -3.507; 0.019 -0.999 0.028 -2.203; 0.000 0.000 0.000 1.000; Loading mov 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 Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.050042 1 -25.0 -25.0 25.0 1.064807 2 -25.0 25.0 -25.0 1.056503 3 -25.0 25.0 25.0 1.049623 4 25.0 -25.0 -25.0 1.039767 5 25.0 -25.0 25.0 0.995306 6 25.0 25.0 -25.0 0.986182 7 25.0 25.0 25.0 1.034912 REL: 8 1.199086 8.277143 1.034643 rel = 1.15894 Initial costs ---------------- Number of surface hits 2314 WM Intensity 4462.4846 +/- 970.3029 Ctx Intensity 4259.3868 +/- 1130.6250 Pct Contrast -6.6946 +/- 20.9085 Cost 1.1991 RelCost 1.1589 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 1.1374 1.1374 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.1169 1.1169 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0841 1.0841 0.0 46 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.0000 1.0711 1.0711 0.0 50 -4.0000 -4.0000 0.0000 4.0000 0.0000 4.0000 1.0708 1.0708 0.0 56 -4.0000 -4.0000 4.0000 -4.0000 -4.0000 4.0000 1.0707 1.0707 0.0 65 -4.0000 -4.0000 4.0000 0.0000 -4.0000 4.0000 1.0694 1.0694 0.0 77 -4.0000 -4.0000 4.0000 4.0000 0.0000 4.0000 1.0662 1.0662 0.0 489 4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 1.0601 1.0601 0.0 490 4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 1.0454 1.0454 0.0 507 4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 1.0412 1.0412 0.0 Brute Force -------------------------- Min cost was 1.041192 Number of iterations 729 Search time 1.143000 sec Parameters at best (transmm, rotdeg) 4.000 -4.000 -4.000 4.000 0.000 -4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 4 1 -4 2 -4 3 4 4 0 5 -4 2 5.000 -4.000 -4.000 4.000 0.000 -4.000 1.0210291764 5 5.618 -4.000 -4.000 4.000 0.000 -4.000 1.0177972868 7 5.505 -4.000 -4.000 4.000 0.000 -4.000 1.0167927969 9 5.492 -4.000 -4.000 4.000 0.000 -4.000 1.0167341843 11 5.470 -4.000 -4.000 4.000 0.000 -4.000 1.0167303654 12 5.480 -4.000 -4.000 4.000 0.000 -4.000 1.0167174622 13 5.481 -4.000 -4.000 4.000 0.000 -4.000 1.0167169452 14 5.484 -4.000 -4.000 4.000 0.000 -4.000 1.0167159633 20 5.484 -5.618 -4.000 4.000 0.000 -4.000 0.9982325285 24 5.484 -5.382 -4.000 4.000 0.000 -4.000 0.9980980321 31 5.484 -5.395 -4.000 4.000 0.000 -4.000 0.9980721270 32 5.484 -5.396 -4.000 4.000 0.000 -4.000 0.9980717801 33 5.484 -5.397 -4.000 4.000 0.000 -4.000 0.9980714840 35 5.484 -5.400 -4.000 4.000 0.000 -4.000 0.9980712285 36 5.484 -5.399 -4.000 4.000 0.000 -4.000 0.9980711784 48 5.484 -5.399 -3.998 4.000 0.000 -4.000 0.9980700736 50 5.484 -5.399 -3.992 4.000 0.000 -4.000 0.9980677036 51 5.484 -5.399 -3.991 4.000 0.000 -4.000 0.9980676829 58 5.484 -5.399 -3.991 4.382 0.000 -4.000 0.9963293879 59 5.484 -5.399 -3.991 4.499 0.000 -4.000 0.9954409177 65 5.484 -5.399 -3.991 4.510 0.000 -4.000 0.9954310224 66 5.484 -5.399 -3.991 4.509 0.000 -4.000 0.9954305460 67 5.484 -5.399 -3.991 4.508 0.000 -4.000 0.9954301631 76 5.484 -5.399 -3.991 4.508 -0.269 -4.000 0.9920621859 77 5.484 -5.399 -3.991 4.508 -0.288 -4.000 0.9920398591 79 5.484 -5.399 -3.991 4.508 -0.286 -4.000 0.9920383614 81 5.484 -5.399 -3.991 4.508 -0.284 -4.000 0.9920376960 92 5.484 -5.399 -3.991 4.508 -0.284 -4.063 0.9920028811 93 5.484 -5.399 -3.991 4.508 -0.284 -4.040 0.9919528000 94 5.484 -5.399 -3.991 4.508 -0.284 -4.036 0.9919511577 95 5.484 -5.399 -3.991 4.508 -0.284 -4.035 0.9919510982 105 5.457 -5.399 -3.991 4.508 -0.284 -4.035 0.9917392100 106 5.440 -5.399 -3.991 4.508 -0.284 -4.035 0.9917028205 108 5.444 -5.399 -3.991 4.508 -0.284 -4.035 0.9916993126 118 5.443 -5.606 -3.991 4.508 -0.284 -4.035 0.9902128207 119 5.443 -5.620 -3.991 4.508 -0.284 -4.035 0.9900863901 120 5.443 -5.772 -3.991 4.508 -0.284 -4.035 0.9900515911 121 5.443 -5.698 -3.991 4.508 -0.284 -4.035 0.9898506126 122 5.443 -5.699 -3.991 4.508 -0.284 -4.035 0.9898502600 123 5.443 -5.703 -3.991 4.508 -0.284 -4.035 0.9898481724 135 5.443 -5.703 -4.134 4.508 -0.284 -4.035 0.9897838752 136 5.443 -5.703 -4.079 4.508 -0.284 -4.035 0.9896793108 138 5.443 -5.703 -4.082 4.508 -0.284 -4.035 0.9896781083 140 5.443 -5.703 -4.088 4.508 -0.284 -4.035 0.9896775140 141 5.443 -5.703 -4.087 4.508 -0.284 -4.035 0.9896774679 142 5.443 -5.703 -4.086 4.508 -0.284 -4.035 0.9896774534 150 5.443 -5.703 -4.086 4.411 -0.284 -4.035 0.9892767800 152 5.443 -5.703 -4.086 4.441 -0.284 -4.035 0.9892606374 154 5.443 -5.703 -4.086 4.429 -0.284 -4.035 0.9892319796 155 5.443 -5.703 -4.086 4.428 -0.284 -4.035 0.9892307497 157 5.443 -5.703 -4.086 4.426 -0.284 -4.035 0.9892305865 165 5.443 -5.703 -4.086 4.426 -0.347 -4.035 0.9890743188 167 5.443 -5.703 -4.086 4.426 -0.352 -4.035 0.9890711732 168 5.443 -5.703 -4.086 4.426 -0.356 -4.035 0.9890673966 170 5.443 -5.703 -4.086 4.426 -0.358 -4.035 0.9890663998 179 5.443 -5.703 -4.086 4.426 -0.358 -4.033 0.9890561399 181 5.443 -5.703 -4.086 4.426 -0.358 -4.005 0.9889640394 183 5.443 -5.703 -4.086 4.426 -0.358 -3.998 0.9889566030 184 5.443 -5.703 -4.086 4.426 -0.358 -3.997 0.9889563175 193 5.323 -5.703 -4.086 4.426 -0.358 -3.997 0.9884430827 194 5.324 -5.703 -4.086 4.426 -0.358 -3.997 0.9884376217 195 5.357 -5.703 -4.086 4.426 -0.358 -3.997 0.9883304160 199 5.355 -5.703 -4.086 4.426 -0.358 -3.997 0.9883298246 219 5.355 -5.702 -4.075 4.426 -0.358 -3.997 0.9883181209 220 5.355 -5.702 -4.059 4.426 -0.358 -3.997 0.9882977961 223 5.355 -5.702 -4.039 4.426 -0.358 -3.997 0.9882948980 224 5.355 -5.702 -4.047 4.426 -0.358 -3.997 0.9882886946 225 5.355 -5.702 -4.048 4.426 -0.358 -3.997 0.9882885640 236 5.355 -5.702 -4.048 4.418 -0.358 -3.997 0.9882885504 238 5.355 -5.702 -4.048 4.422 -0.358 -3.997 0.9882866012 252 5.355 -5.702 -4.048 4.422 -0.359 -3.997 0.9882865428 260 5.355 -5.702 -4.048 4.422 -0.359 -3.974 0.9882710035 261 5.355 -5.702 -4.048 4.422 -0.359 -3.977 0.9882703407 274 5.353 -5.702 -4.048 4.422 -0.359 -3.977 0.9882680269 275 5.352 -5.702 -4.048 4.422 -0.359 -3.977 0.9882672992 286 5.352 -5.699 -4.048 4.422 -0.359 -3.977 0.9882670080 289 5.352 -5.700 -4.048 4.422 -0.359 -3.977 0.9882669172 302 5.352 -5.700 -4.046 4.422 -0.359 -3.977 0.9882656601 314 5.352 -5.700 -4.046 4.426 -0.359 -3.977 0.9882640401 315 5.352 -5.700 -4.046 4.427 -0.359 -3.977 0.9882637590 326 5.352 -5.700 -4.046 4.427 -0.366 -3.977 0.9882625595 327 5.352 -5.700 -4.046 4.427 -0.363 -3.977 0.9882620748 328 5.352 -5.700 -4.046 4.427 -0.364 -3.977 0.9882619706 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.000086 1 -25.0 -25.0 25.0 1.081853 2 -25.0 25.0 -25.0 1.065790 3 -25.0 25.0 25.0 1.044714 4 25.0 -25.0 -25.0 1.035354 5 25.0 -25.0 25.0 1.007647 6 25.0 25.0 -25.0 0.983068 7 25.0 25.0 25.0 1.071051 REL: 8 0.988262 8.289562 1.036195 rel = 0.953741 Number of iterations 3 Min cost was 0.988262 Number of FunctionCalls 340 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.713000 sec Parameters at optimum (transmm) 5.35153 -5.70023 -4.04595 Parameters at optimum (rotdeg) 4.42659 -0.36422 -3.97675 Final costs ---------------- Number of surface hits 2314 WM Intensity 4029.6846 +/- 1302.1375 Ctx Intensity 3962.0675 +/- 1404.6116 Pct Contrast -4.5892 +/- 27.9683 Cost 0.9883 RelCost 1.1589 Reg at min cost was 0.993 0.034 0.110 7.722; -0.113 0.102 0.988 -9.200; 0.022 -0.994 0.105 -6.497; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/001/tmp.bbregister.4942/bbr.pass1.dat, type = 14 Original Reg 0.999 0.020 0.042 2.592; -0.043 0.027 0.999 -3.507; 0.019 -0.999 0.028 -2.203; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.006 -0.013 -0.068 -5.130; 0.071 -0.075 0.010 5.693; -0.003 -0.005 -0.077 4.294; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 9.274299 Computing change in rh position Surface RMS Diff (mm) 10.314232 15.447315 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 bold/001/tmp.bbregister.4942/template.nii --init-reg bold/001/tmp.bbregister.4942/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --cur-reg bold/001/tmp.bbregister.4942/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /home/pati/Freesurfer/subjects cd /home/pati/Freesurfer/NCN_rest/Neuro_rest_ST/Sub_001 mri_segreg --mov bold/001/tmp.bbregister.4942/template.nii --init-reg bold/001/tmp.bbregister.4942/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --cur-reg bold/001/tmp.bbregister.4942/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname luria machine x86_64 user pati movvol bold/001/tmp.bbregister.4942/template.nii regfile bold/001/tmp.bbregister.4942/bbr.pass1.dat subject Sub_001 dof 6 outregfile bold/001/register.dof6.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 1526890381 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.993 0.034 0.110 7.722; -0.113 0.102 0.988 -9.200; 0.022 -0.994 0.105 -6.497; 0.000 0.000 0.000 1.000; Loading mov 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 Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.019543 1 -25.0 -25.0 25.0 1.082976 2 -25.0 25.0 -25.0 1.038617 3 -25.0 25.0 25.0 1.045365 4 25.0 -25.0 -25.0 1.019719 5 25.0 -25.0 25.0 1.028700 6 25.0 25.0 -25.0 1.016730 7 25.0 25.0 25.0 1.059613 REL: 8 1.009055 8.311264 1.038908 rel = 0.971265 Initial costs ---------------- Number of surface hits 231372 WM Intensity 3995.2618 +/- 1309.1478 Ctx Intensity 3922.0302 +/- 1408.0066 Pct Contrast -4.5865 +/- 27.5058 Cost 1.0091 RelCost 0.9713 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 0.9914 0.9914 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.9903 0.9903 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.9901 0.9901 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.9898 0.9898 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.9896 0.9896 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.9893 0.9893 0.0 43 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.0000 0.9891 0.9891 0.0 91 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.9890 0.9890 0.0 93 -0.1000 0.0000 -0.1000 0.0000 0.0000 -0.1000 0.9888 0.9888 0.0 334 0.0000 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.9886 0.9886 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.9885 0.9885 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.9883 0.9883 0.0 Brute Force -------------------------- Min cost was 0.988262 Number of iterations 729 Search time 0.914000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 2 1.000 0.000 0.000 0.000 0.000 0.000 1.0016804024 5 1.618 0.000 0.000 0.000 0.000 0.000 1.0013901223 7 1.448 0.000 0.000 0.000 0.000 0.000 1.0012423064 8 1.388 0.000 0.000 0.000 0.000 0.000 1.0012306694 11 1.393 0.000 0.000 0.000 0.000 0.000 1.0012299724 17 1.395 -1.618 0.000 0.000 0.000 0.000 0.9951025159 21 1.395 -2.618 0.000 0.000 0.000 0.000 0.9920469593 33 1.395 -2.618 -1.618 0.000 0.000 0.000 0.9888018345 39 1.395 -2.618 -1.713 0.000 0.000 0.000 0.9887141233 41 1.395 -2.618 -1.804 0.000 0.000 0.000 0.9887073581 42 1.395 -2.618 -1.766 0.000 0.000 0.000 0.9886701768 44 1.395 -2.618 -1.767 0.000 0.000 0.000 0.9886700671 47 1.395 -2.618 -1.769 0.000 0.000 0.000 0.9886699894 51 1.395 -2.618 -1.770 -1.618 0.000 0.000 0.9805835468 58 1.395 -2.618 -1.770 -1.615 0.000 0.000 0.9805832030 62 1.395 -2.618 -1.770 -1.614 1.000 0.000 0.9774875432 65 1.395 -2.618 -1.770 -1.614 1.618 0.000 0.9769318325 67 1.395 -2.618 -1.770 -1.614 1.530 0.000 0.9769132248 70 1.395 -2.618 -1.770 -1.614 1.531 0.000 0.9769130252 72 1.395 -2.618 -1.770 -1.614 1.533 0.000 0.9769130148 79 1.395 -2.618 -1.770 -1.614 1.533 0.382 0.9767276163 80 1.395 -2.618 -1.770 -1.614 1.533 0.323 0.9766945409 81 1.395 -2.618 -1.770 -1.614 1.533 0.266 0.9766713187 95 0.777 -2.618 -1.770 -1.614 1.533 0.266 0.9757441111 97 0.915 -2.618 -1.770 -1.614 1.533 0.266 0.9755400629 101 0.914 -2.618 -1.770 -1.614 1.533 0.266 0.9755399419 102 0.910 -2.618 -1.770 -1.614 1.533 0.266 0.9755397683 103 0.911 -2.618 -1.770 -1.614 1.533 0.266 0.9755397103 109 0.911 -3.236 -1.770 -1.614 1.533 0.266 0.9750760216 111 0.911 -3.133 -1.770 -1.614 1.533 0.266 0.9748826838 113 0.911 -3.070 -1.770 -1.614 1.533 0.266 0.9748795597 114 0.911 -3.096 -1.770 -1.614 1.533 0.266 0.9748736740 118 0.911 -3.095 -1.770 -1.614 1.533 0.266 0.9748730940 119 0.911 -3.094 -1.770 -1.614 1.533 0.266 0.9748726123 121 0.911 -3.094 -0.770 -1.614 1.533 0.266 0.9739789937 128 0.911 -3.094 -0.703 -1.614 1.533 0.266 0.9738918271 134 0.911 -3.094 -0.701 -1.614 1.533 0.266 0.9738916749 135 0.911 -3.094 -0.702 -1.614 1.533 0.266 0.9738916508 138 0.911 -3.094 -0.702 -3.232 1.533 0.266 0.9735761037 139 0.911 -3.094 -0.702 -2.470 1.533 0.266 0.9727820621 141 0.911 -3.094 -0.702 -2.143 1.533 0.266 0.9727776168 143 0.911 -3.094 -0.702 -2.305 1.533 0.266 0.9725983974 144 0.911 -3.094 -0.702 -2.306 1.533 0.266 0.9725976674 145 0.911 -3.094 -0.702 -2.369 1.533 0.266 0.9725670426 148 0.911 -3.094 -0.702 -2.367 1.533 0.266 0.9725657560 150 0.911 -3.094 -0.702 -2.364 1.533 0.266 0.9725633766 151 0.911 -3.094 -0.702 -2.363 1.533 0.266 0.9725629240 152 0.911 -3.094 -0.702 -2.361 1.533 0.266 0.9725623920 153 0.911 -3.094 -0.702 -2.360 1.533 0.266 0.9725622023 160 0.911 -3.094 -0.702 -2.360 1.721 0.266 0.9724716608 161 0.911 -3.094 -0.702 -2.360 1.719 0.266 0.9724703601 162 0.911 -3.094 -0.702 -2.360 1.668 0.266 0.9724386935 166 0.911 -3.094 -0.702 -2.360 1.669 0.266 0.9724385493 167 0.911 -3.094 -0.702 -2.360 1.670 0.266 0.9724385370 176 0.911 -3.094 -0.702 -2.360 1.670 0.403 0.9723441166 178 0.911 -3.094 -0.702 -2.360 1.670 0.370 0.9722958264 179 0.911 -3.094 -0.702 -2.360 1.670 0.351 0.9722851939 183 0.911 -3.094 -0.702 -2.360 1.670 0.352 0.9722847162 184 0.911 -3.094 -0.702 -2.360 1.670 0.353 0.9722842169 192 0.706 -3.094 -0.702 -2.360 1.670 0.353 0.9718444707 195 0.709 -3.094 -0.702 -2.360 1.670 0.353 0.9718438903 196 0.711 -3.094 -0.702 -2.360 1.670 0.353 0.9718436266 198 0.712 -3.094 -0.702 -2.360 1.670 0.353 0.9718435789 208 0.713 -3.109 -0.702 -2.360 1.670 0.353 0.9718390469 211 0.713 -3.105 -0.702 -2.360 1.670 0.353 0.9718355784 213 0.713 -3.106 -0.702 -2.360 1.670 0.353 0.9718351900 214 0.713 -3.107 -0.702 -2.360 1.670 0.353 0.9718348383 221 0.713 -3.107 -0.515 -2.360 1.670 0.353 0.9716844700 223 0.713 -3.107 -0.550 -2.360 1.670 0.353 0.9716731497 224 0.713 -3.107 -0.608 -2.360 1.670 0.353 0.9716631170 227 0.713 -3.107 -0.616 -2.360 1.670 0.353 0.9716627641 229 0.713 -3.107 -0.612 -2.360 1.670 0.353 0.9716615797 241 0.713 -3.107 -0.612 -2.350 1.670 0.353 0.9716591929 243 0.713 -3.107 -0.612 -2.351 1.670 0.353 0.9716591510 251 0.713 -3.107 -0.612 -2.351 1.766 0.353 0.9715914506 252 0.713 -3.107 -0.612 -2.351 1.770 0.353 0.9715912953 254 0.713 -3.107 -0.612 -2.351 1.773 0.353 0.9715912696 258 0.713 -3.107 -0.612 -2.351 1.798 0.353 0.9715890326 260 0.713 -3.107 -0.612 -2.351 1.800 0.353 0.9715888115 271 0.713 -3.107 -0.612 -2.351 1.800 0.388 0.9715684195 272 0.713 -3.107 -0.612 -2.351 1.800 0.389 0.9715678187 274 0.713 -3.107 -0.612 -2.351 1.800 0.397 0.9715665048 275 0.713 -3.107 -0.612 -2.351 1.800 0.396 0.9715662595 276 0.713 -3.107 -0.612 -2.351 1.800 0.395 0.9715662347 278 0.515 -3.120 -0.523 -2.343 1.930 0.437 0.9715373550 284 0.590 -3.115 -0.557 -2.346 1.881 0.421 0.9715329563 291 0.591 -3.115 -0.557 -2.346 1.880 0.421 0.9715328227 293 0.592 -3.115 -0.558 -2.346 1.880 0.420 0.9715327311 294 0.592 -3.115 -0.558 -2.346 1.880 0.420 0.9715327152 306 0.592 -3.115 -0.558 -2.346 1.879 0.427 0.9715309732 309 0.592 -3.115 -0.558 -2.346 1.879 0.433 0.9715304377 319 0.592 -3.366 -0.558 -2.346 1.879 0.432 0.9714057784 321 0.592 -3.506 -0.558 -2.346 1.879 0.432 0.9713909947 322 0.592 -3.441 -0.558 -2.346 1.879 0.432 0.9713531452 323 0.592 -3.442 -0.558 -2.346 1.879 0.432 0.9713528050 325 0.592 -3.446 -0.558 -2.346 1.879 0.432 0.9713519098 328 0.592 -3.447 -0.558 -2.346 1.879 0.432 0.9713519055 334 0.592 -3.447 -0.176 -2.346 1.879 0.432 0.9711670418 338 0.592 -3.447 -0.180 -2.346 1.879 0.432 0.9711662074 339 0.592 -3.447 -0.182 -2.346 1.879 0.432 0.9711660142 341 0.592 -3.447 -0.185 -2.346 1.879 0.432 0.9711658533 344 0.592 -3.447 -0.186 -2.346 1.879 0.432 0.9711658426 351 0.592 -3.447 -0.186 -2.619 1.879 0.432 0.9706735673 352 0.592 -3.447 -0.186 -2.636 1.879 0.432 0.9706194119 354 0.592 -3.447 -0.186 -2.686 1.879 0.432 0.9705475642 356 0.592 -3.447 -0.186 -2.675 1.879 0.432 0.9705417276 357 0.592 -3.447 -0.186 -2.674 1.879 0.432 0.9705412056 360 0.592 -3.447 -0.186 -2.672 1.879 0.432 0.9705406060 362 0.592 -3.447 -0.186 -2.673 1.879 0.432 0.9705403793 369 0.592 -3.447 -0.186 -2.673 1.905 0.432 0.9705391799 370 0.592 -3.447 -0.186 -2.673 1.896 0.432 0.9705340135 371 0.592 -3.447 -0.186 -2.673 1.893 0.432 0.9705335986 373 0.592 -3.447 -0.186 -2.673 1.894 0.432 0.9705335275 381 0.559 -3.450 -0.171 -2.672 1.916 0.439 0.9705298307 384 0.557 -3.450 -0.170 -2.672 1.917 0.440 0.9705291075 385 0.552 -3.450 -0.168 -2.671 1.921 0.441 0.9705284434 386 0.552 -3.450 -0.168 -2.671 1.921 0.441 0.9705283994 387 0.552 -3.450 -0.168 -2.671 1.920 0.441 0.9705283809 390 0.553 -3.450 -0.168 -2.671 1.920 0.441 0.9705283422 401 0.553 -3.450 -0.168 -2.671 1.920 0.386 0.9704806471 402 0.553 -3.450 -0.168 -2.671 1.920 0.382 0.9704802526 403 0.553 -3.450 -0.168 -2.671 1.920 0.380 0.9704802401 405 0.553 -3.450 -0.168 -2.671 1.920 0.381 0.9704802150 417 0.553 -3.443 -0.168 -2.671 1.920 0.381 0.9704785868 429 0.553 -3.443 -0.124 -2.671 1.920 0.381 0.9704609198 430 0.553 -3.443 -0.127 -2.671 1.920 0.381 0.9704594850 431 0.553 -3.443 -0.137 -2.671 1.920 0.381 0.9704540198 433 0.553 -3.443 -0.140 -2.671 1.920 0.381 0.9704538350 444 0.553 -3.443 -0.141 -2.667 1.920 0.381 0.9704523815 447 0.553 -3.443 -0.141 -2.666 1.920 0.381 0.9704521177 456 0.553 -3.443 -0.141 -2.666 1.901 0.381 0.9704519755 457 0.553 -3.443 -0.141 -2.666 1.910 0.381 0.9704493171 458 0.553 -3.443 -0.141 -2.666 1.911 0.381 0.9704492076 468 0.542 -3.444 -0.136 -2.666 1.918 0.383 0.9704449663 471 0.537 -3.444 -0.134 -2.665 1.922 0.384 0.9704431046 472 0.536 -3.444 -0.133 -2.665 1.922 0.384 0.9704427921 473 0.533 -3.445 -0.132 -2.665 1.925 0.385 0.9704427586 474 0.534 -3.444 -0.132 -2.665 1.924 0.385 0.9704425844 475 0.534 -3.444 -0.132 -2.665 1.924 0.385 0.9704425776 476 0.534 -3.445 -0.132 -2.665 1.924 0.385 0.9704425607 488 0.534 -3.445 -0.132 -2.665 1.924 0.367 0.9704369129 489 0.534 -3.445 -0.132 -2.665 1.924 0.368 0.9704368845 490 0.534 -3.445 -0.132 -2.665 1.924 0.369 0.9704368657 506 0.534 -3.444 -0.132 -2.665 1.924 0.370 0.9704368288 517 0.534 -3.444 -0.130 -2.665 1.924 0.370 0.9704363291 518 0.534 -3.444 -0.129 -2.665 1.924 0.370 0.9704362142 541 0.534 -3.444 -0.128 -2.665 1.926 0.370 0.9704358302 554 0.539 -3.443 -0.130 -2.666 1.925 0.369 0.9704349909 555 0.539 -3.443 -0.130 -2.666 1.925 0.369 0.9704349577 556 0.538 -3.443 -0.130 -2.666 1.926 0.369 0.9704349512 570 0.537 -3.443 -0.129 -2.666 1.926 0.363 0.9704344479 571 0.537 -3.443 -0.129 -2.666 1.926 0.364 0.9704344006 572 0.537 -3.443 -0.129 -2.666 1.926 0.365 0.9704343432 587 0.537 -3.445 -0.129 -2.666 1.926 0.365 0.9704343092 599 0.537 -3.445 -0.127 -2.666 1.926 0.365 0.9704341911 612 0.537 -3.445 -0.126 -2.667 1.926 0.365 0.9704340394 622 0.537 -3.445 -0.126 -2.667 1.928 0.365 0.9704337460 623 0.537 -3.445 -0.126 -2.667 1.929 0.365 0.9704336778 635 0.538 -3.445 -0.127 -2.667 1.930 0.365 0.9704336295 636 0.538 -3.445 -0.127 -2.667 1.930 0.365 0.9704336200 640 0.539 -3.445 -0.127 -2.667 1.930 0.365 0.9704336028 652 0.538 -3.445 -0.127 -2.667 1.930 0.363 0.9704333944 681 0.538 -3.445 -0.126 -2.667 1.930 0.363 0.9704333596 795 0.538 -3.445 -0.126 -2.667 1.930 0.363 0.9704333567 796 0.539 -3.445 -0.126 -2.667 1.929 0.362 0.9704333071 863 0.539 -3.445 -0.126 -2.667 1.930 0.362 0.9704332694 Powell done niters = 9 Computing relative cost 0 -25.0 -25.0 -25.0 1.001170 1 -25.0 -25.0 25.0 1.043650 2 -25.0 25.0 -25.0 1.017634 3 -25.0 25.0 25.0 1.048857 4 25.0 -25.0 -25.0 1.027976 5 25.0 -25.0 25.0 1.056034 6 25.0 25.0 -25.0 1.021217 7 25.0 25.0 25.0 1.055079 REL: 8 0.970433 8.271617 1.033952 rel = 0.938567 Number of iterations 9 Min cost was 0.970433 Number of FunctionCalls 876 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 44.434000 sec Parameters at optimum (transmm) 0.53879 -3.44453 -0.12611 Parameters at optimum (rotdeg) -2.66657 1.93036 0.36244 Final costs ---------------- Number of surface hits 231155 WM Intensity 3797.2272 +/- 1518.1774 Ctx Intensity 3756.9296 +/- 1571.3260 Pct Contrast -3.2040 +/- 30.1922 Cost 0.9704 RelCost 0.9713 Reg at min cost was 0.994 -0.000 0.106 8.113; -0.106 0.056 0.993 -12.889; -0.006 -0.998 0.056 -6.445; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/001/register.dof6.dat, type = 14 Original Reg 0.993 0.034 0.110 7.722; -0.113 0.102 0.988 -9.200; 0.022 -0.994 0.105 -6.497; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.001 0.034 0.004 -0.390; -0.007 0.046 -0.005 3.689; 0.028 0.004 0.050 -0.052; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 4.023809 Computing change in rh position Surface RMS Diff (mm) 3.910001 7.175295 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 Cleaning up Started at Sat May 12 13:11:31 CEST 2018 Ended at Sat May 12 13:12:44 CEST 2018 BBR-Run-Time-Sec 73 bbregister Done To check results, run: tkregister2 --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --surf
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.