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
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