EDIT: I’m a new user so I’ve hit the reply limit. Your comment below is correct. I’m now running on a high memory node and am not having any issues. That said, my issue may have been different from the one faced by the original poster.
recon-all.log (just the end due to character limit)
mri_convert --no_scale 1 /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/T2raw.mgz
mri_convert.bin --no_scale 1 /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/T2raw.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T2w_acpc_dc_restore.nii.gz...
TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/T2raw.mgz...
#--------------------------------------------
#@# MotionCor Wed Jun 16 09:59:20 CDT 2021
Found 1 runs
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig/001.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001
mri_convert /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz --conform
mri_convert.bin /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/rawavg.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz...
mri_add_xform_to_header -c /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/transforms/talairach.xfm /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz
INFO: extension is mgz
mri_vol2vol --mov /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz --targ /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz --regheader --interp nearest --o /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/extern.emreg.mask.mgz
movvol /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/T1w_acpc_dc_restore_brain.nii.gz
targvol /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/orig.mgz
outvol /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/extern.emreg.mask.mgz
invert 0
tal 0
talres 2
regheader 1
noresample 0
interp nearest (0)
precision float (3)
Gdiag_no -1
Synth 0
SynthSeed 1624712569
Computing registration based on scanner-to-scanner
Final tkRAS-to-tkRAS Matrix is:
1.00000 0.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 -1.00000 0.00000 -0.00001;
0.00000 0.00000 0.00000 1.00000;
Vox2Vox Matrix is:
1.42857 0.00000 0.00000 -52.85715;
0.00000 0.00000 1.42857 -27.35713;
0.00000 -1.42857 0.00000 312.85715;
0.00000 0.00000 0.00000 1.00000;
Resampling
Output registration matrix is identity
mri_vol2vol done
#--------------------------------------------
#@# Talairach Wed Jun 16 09:59:33 CDT 2021
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
/opt/freesurfer/freesurfer-6.0/bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux ln0004 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Wed Jun 16 09:59:33 CDT 2021
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.520195
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.520195/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.520195/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.520195/nu0.mnc...
--------------------------------------------------------
Iteration 1 Wed Jun 16 09:59:35 CDT 2021
nu_correct -clobber ./tmp.mri_nu_correct.mni.520195/nu0.mnc ./tmp.mri_nu_correct.mni.520195/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.520195/0/ -iterations 1000 -distance 50
[roedi004@ln0004:/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/] [2021-06-16 09:59:35] running:
/opt/freesurfer/freesurfer-6.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.520195/0/ ./tmp.mri_nu_correct.mni.520195/nu0.mnc ./tmp.mri_nu_correct.mni.520195/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
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Processing:.................................................................Done
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Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 25
CV of field change: 0.000996372
mri_convert ./tmp.mri_nu_correct.mni.520195/nu1.mnc orig_nu.mgz --like orig.mgz --conform
mri_convert.bin ./tmp.mri_nu_correct.mni.520195/nu1.mnc orig_nu.mgz --like orig.mgz --conform
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.520195/nu1.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
writing to orig_nu.mgz...
Wed Jun 16 10:00:29 CDT 2021
mri_nu_correct.mni done
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
talairach_avi log file is transforms/talairach_avi.log...
Started at Wed Jun 16 10:00:29 CDT 2021
Ended at Wed Jun 16 10:01:02 CDT 2021
talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Wed Jun 16 10:01:04 CDT 2021
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7258, pval=0.6675 >= threshold=0.0050)
awk -f /opt/freesurfer/freesurfer-6.0/bin/extract_talairach_avi_QA.awk /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/transforms/talairach_avi.log
tal_QC_AZS /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/transforms/talairach_avi.log
TalAviQA: 0.96889
z-score: -2
#--------------------------------------------
#@# Nu Intensity Correction Wed Jun 16 10:01:04 CDT 2021
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
/opt/freesurfer/freesurfer-6.0/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux ln0004 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
Wed Jun 16 10:01:04 CDT 2021
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.521075
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.521075/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.521075/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.521075/nu0.mnc...
--------------------------------------------------------
Iteration 1 Wed Jun 16 10:01:10 CDT 2021
nu_correct -clobber ./tmp.mri_nu_correct.mni.521075/nu0.mnc ./tmp.mri_nu_correct.mni.521075/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.521075/0/
[roedi004@ln0004:/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/] [2021-06-16 10:01:10] running:
/opt/freesurfer/freesurfer-6.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.521075/0/ ./tmp.mri_nu_correct.mni.521075/nu0.mnc ./tmp.mri_nu_correct.mni.521075/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 18
CV of field change: 0.000972136
--------------------------------------------------------
Iteration 2 Wed Jun 16 10:01:57 CDT 2021
nu_correct -clobber ./tmp.mri_nu_correct.mni.521075/nu1.mnc ./tmp.mri_nu_correct.mni.521075/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.521075/1/
[roedi004@ln0004:/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/] [2021-06-16 10:01:57] running:
/opt/freesurfer/freesurfer-6.0/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.521075/1/ ./tmp.mri_nu_correct.mni.521075/nu1.mnc ./tmp.mri_nu_correct.mni.521075/nu2.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Number of iterations: 7
CV of field change: 0.000992815
mri_binarize --i ./tmp.mri_nu_correct.mni.521075/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.521075/ones.mgz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.521075/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.521075/ones.mgz
sysname Linux
hostname ln0004
machine x86_64
user roedi004
input ./tmp.mri_nu_correct.mni.521075/nu2.mnc
frame 0
nErode3d 0
nErode2d 0
output ./tmp.mri_nu_correct.mni.521075/ones.mgz
Binarizing based on threshold
min -1
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 16777216 values in range
Counting number of voxels in first frame
Found 16777216 voxels in final mask
Count: 16777216 16777216.000000 16777216 100.000000
mri_binarize done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.521075/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.521075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.521075/input.mean.dat
$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.521075/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.521075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.521075/input.mean.dat
sysname Linux
hostname ln0004
machine x86_64
user roedi004
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.521075/ones.mgz
Loading orig.mgz
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.521075/input.mean.dat
mri_segstats done
mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.521075/ones.mgz --i ./tmp.mri_nu_correct.mni.521075/nu2.mnc --sum ./tmp.mri_nu_correct.mni.521075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.521075/output.mean.dat
$Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $
cwd
cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.521075/ones.mgz --i ./tmp.mri_nu_correct.mni.521075/nu2.mnc --sum ./tmp.mri_nu_correct.mni.521075/sum.junk --avgwf ./tmp.mri_nu_correct.mni.521075/output.mean.dat
sysname Linux
hostname ln0004
machine x86_64
user roedi004
UseRobust 0
Loading ./tmp.mri_nu_correct.mni.521075/ones.mgz
Loading ./tmp.mri_nu_correct.mni.521075/nu2.mnc
Voxel Volume is 1 mm^3
Generating list of segmentation ids
Found 1 segmentations
Computing statistics for each segmentation
Reporting on 1 segmentations
Using PrintSegStat
Computing spatial average of each frame
0
Writing to ./tmp.mri_nu_correct.mni.521075/output.mean.dat
mri_segstats done
mris_calc -o ./tmp.mri_nu_correct.mni.521075/nu2.mnc ./tmp.mri_nu_correct.mni.521075/nu2.mnc mul .92391690360540490099
Saving result to './tmp.mri_nu_correct.mni.521075/nu2.mnc' (type = MINC ) [ ok ]
mri_convert ./tmp.mri_nu_correct.mni.521075/nu2.mnc nu.mgz --like orig.mgz
mri_convert.bin ./tmp.mri_nu_correct.mni.521075/nu2.mnc nu.mgz --like orig.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from ./tmp.mri_nu_correct.mni.521075/nu2.mnc...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
INFO: transform src into the like-volume: orig.mgz
writing to nu.mgz...
mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz
type change took 0 minutes and 7 seconds.
mapping (36, 199) to ( 3, 110)
Wed Jun 16 10:03:07 CDT 2021
mri_nu_correct.mni done
mri_add_xform_to_header -c /home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri/transforms/talairach.xfm nu.mgz nu.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Intensity Normalization Wed Jun 16 10:03:08 CDT 2021
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
mri_normalize -g 1 -mprage nu.mgz T1.mgz
using max gradient = 1.000
assuming input volume is MGH (Van der Kouwe) MP-RAGE
reading from nu.mgz...
normalizing image...
talairach transform
1.25969 -0.00441 -0.00714 -0.54750;
0.02505 1.18646 0.10081 1.56232;
0.04489 -0.07770 1.36300 -2.36977;
0.00000 0.00000 0.00000 1.00000;
processing without aseg, no1d=0
MRInormInit():
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize():
MRIsplineNormalize(): npeaks = 19
Starting OpenSpline(): npoints = 19
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Iterating 2 times
---------------------------------
3d normalization pass 1 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 65 (65), valley at 31 (31)
csf peak at 33, setting threshold to 54
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
---------------------------------
3d normalization pass 2 of 2
white matter peak found at 110
white matter peak found at 110
gm peak at 66 (66), valley at 31 (31)
csf peak at 34, setting threshold to 55
building Voronoi diagram...
performing soap bubble smoothing, sigma = 8...
Done iterating ---------------------------------
writing output to T1.mgz
3D bias adjustment took 1 minutes and 58 seconds.
#--------------------------------------------
#@# Skull Stripping Wed Jun 16 10:05:06 CDT 2021
/home/wozniakj/roedi004/qunex/quickstart/sessions/HCPA001/hcp/HCPA001/T1w/HCPA001/mri
mri_em_register -mask extern.emreg.mask.mgz nu.mgz /opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach_with_externmask.lta
using MR volume extern.emreg.mask.mgz to mask input volume...
== Number of threads available to mri_em_register for OpenMP = 8 ==
reading 1 input volumes...
logging results to talairach_with_externmask.log
reading '/opt/freesurfer/freesurfer-6.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3 using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
accounting for voxel sizes in initial transform
bounding unknown intensity as < 6.3 or > 503.7
total sample mean = 78.5 (494 zeros)
************************************************
spacing=8, using 2252 sample points, tol=1.00e-05...
************************************************
register_mri: find_optimal_transform
find_optimal_transform: nsamples 2252, passno 0, spacing 8
resetting wm mean[0]: 98 --> 107
resetting gm mean[0]: 61 --> 61
input volume #1 is the most T1-like
using real data threshold=29.1
skull bounding box = (66, 90, 49) --> (187, 199, 204)
using (106, 126, 127) as brain centroid...
mean wm in atlas = 107, using box (91,113,108) --> (120, 139,146) to find MRI wm
before smoothing, mri peak at 105
robust fit to distribution - 105 +- 4.5
after smoothing, mri peak at 106, scaling input intensities by 1.009
scaling channel 0 by 1.00943
initial log_p = -4.858
************************************************
First Search limited to translation only.
************************************************
max log p = -4.535702 @ (-9.091, -27.273, -27.273)
max log p = -4.357319 @ (4.545, 4.545, 13.636)
max log p = -4.256121 @ (2.273, -2.273, -2.273)
max log p = -4.247165 @ (-1.136, 1.136, 3.409)
max log p = -4.236141 @ (1.705, -1.705, -3.977)
max log p = -4.226527 @ (0.284, 0.284, -1.989)
Found translation: (-1.4, -25.3, -18.5): log p = -4.227
****************************************
Nine parameter search. iteration 0 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.726, old_max_log_p =-4.227 (thresh=-4.2)
1.15000 0.00000 0.00000 -20.64408;
0.00000 1.22567 -0.14032 -33.02412;
0.00000 0.16136 1.06580 -49.94852;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 1 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.668, old_max_log_p =-3.726 (thresh=-3.7)
1.15000 0.00000 0.00000 -20.64408;
0.00000 1.31760 -0.15084 -44.44769;
0.00000 0.16136 1.06580 -49.94852;
0.00000 0.00000 0.00000 1.00000;
****************************************
Nine parameter search. iteration 2 nscales = 0 ...
****************************************
Result so far: scale 1.000: max_log_p=-3.668, old_max_log_p =-3.668 (thresh=-3.7)
1.15000 0.00000 0.00000 -20.64408;
0.00000 1.31760 -0.15084 -44.44769;
0.00000 0.16136 1.06580 -49.94852;
0.00000 0.00000 0.00000 1.00000;
reducing scale to 0.2500
****************************************
Nine parameter search. iteration 3 nscales = 1 ...
****************************************
Terminated
Linux ln0004 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s HCPA001 exited with ERRORS at Wed Jun 16 10:13:01 CDT 2021
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