I'm attempting to run preproc-sess and have got an error - it seems while running mri_vol2surf. I've included the full output of preproc-sess below, but I think the key information will be right at the end where the error message is.
A couple of comments that may be relevant:
- The raw data I've placed in the directory are links to the files that were created using the bash ln -s command
- They are in nii.gz format
really briefly, the key information seems to be:
-------
niiRead(): error reading from /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz
srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz
srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilin
float2int = round
GetProjMax = 0
INFO: float2int code = 0
ERROR: Read 13, expected 64
ERROR: could not read /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz as type 24
------
Any ideas? Thanks very much in advance for your help!
Ben
--------------------------------------------------------------
preproc-sess logfile is log/preproc-sess.20592.log
--------------------------------------------------------------
$Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $
bensmith
setenv FREESURFER_HOME /opt/fmritools/freesurfer
setenv SUBJECTS_DIR /opt/fmritools/freesurfer/subjects
Linux msm2 4.12.0-1-amd64 #1 SMP Debian 4.12.6-1 (2017-08-12) x86_64 GNU/Linux
/expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed
/opt/fmritools/freesurfer/fsfast/bin/preproc-sess
-sf sessid -fsd bold -surface fsaverage lhrh -mni305 -fwhm 5 -per-run
Sun Feb 11 14:19:19 PST 2018
instem f
mc 1 f fmcpr
stc 0 fmcpr
sm 0
mask 1 brain
sub106sess Template -----------------------------
mktemplate-sess -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -fsd bold -update
Session: /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess ----------------
Sun Feb 11 14:19:20 PST 2018
Detected input format at nii.gz
sub106sess Update not needed
Run: 001 ----------------
Sun Feb 11 14:19:20 PST 2018
sub106sess 001 Update not needed
Run: 002 ----------------
Sun Feb 11 14:19:20 PST 2018
sub106sess 002 Update not needed
Sun Feb 11 14:19:20 PST 2018
mktemplate-sess completed
sub106sess Registration -----------------------------
register-sess -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg
--------------------------------------------------------------
register-sess logfile is /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/log/register-sess.sub106sess.log
--------------------------------------------------------------
Sun Feb 11 14:19:20 PST 2018
setenv SUBJECTS_DIR /opt/fmritools/freesurfer/subjects
cd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed
/opt/fmritools/freesurfer/fsfast/bin/register-sess -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux msm2 4.12.0-1-amd64 #1 SMP Debian 4.12.6-1 (2017-08-12) x86_64 GNU/Linux
Session: /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess ----------------
Sun Feb 11 14:19:20 PST 2018
/expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess
Run: 001 ----------------
Sun Feb 11 14:19:20 PST 2018
Update not needed
Run: 002 ----------------
Sun Feb 11 14:19:21 PST 2018
Update not needed
Sun Feb 11 14:19:21 PST 2018
register-sess completed
sub106sess Mask ------------------------
mkbrainmask-sess -maskstem brain -fsd bold -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -per-run -update
------------------------------------------------
/expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess
Sun Feb 11 14:19:21 PST 2018
sub106sess Update not needed for session-level mask
sub106sess Update not needed for run 001 mask
sub106sess Update not needed for run 002 mask
sub106sess Update not needed for run 001 meanval
sub106sess Update not needed for run 002 meanval
Sun Feb 11 14:19:21 PST 2018
mkbrainmask-sess done
sub106sess MC -----------------------------
mc-sess -fstem f -fmcstem fmcpr -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -fsd bold -per-run -update
Logfile is /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/log/mc-sub106sess-bold.log
-------------------------------------------
/expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess
RunList: 001 002
sub106sess 001 Update not needed
------- ************************** -----------
------- Motion Correcting Run 002 -----------
------- ************************** -----------
sess = sub106sess
Sun Feb 11 14:19:22 PST 2018
mc-afni2 --i 002/f.nii.gz --t 002/template.nii.gz --o 002/fmcpr.nii.gz --mcdat 002/fmcpr.mcdat
/expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold
mri_info --nframes --o /tmp/mriinfo.21157 002/template.nii.gz
log file is 002/fmcpr.nii.gz.mclog
mcdat file is 002/fmcpr.mcdat
tmp dir is 002/tmp.mc-afni2.21157
#@# --------------------------------
/expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold
mri_convert 002/template.nii.gz 002/tmp.mc-afni2.21157/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float
mri_convert.bin 002/template.nii.gz 002/tmp.mc-afni2.21157/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float
nskip = 0
ndrop = 0
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 002/template.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0.946649, 0.322266)
k_ras = (0, -0.322266, 0.946649)
writing to 002/tmp.mc-afni2.21157/tempvol.nii.gz...
#@# --------------------------------
/expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold
mri_convert 002/f.nii.gz 002/tmp.mc-afni2.21157/invol.nii.gz -odt float
mri_convert.bin 002/f.nii.gz 002/tmp.mc-afni2.21157/invol.nii.gz -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 002/f.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0.946649, 0.322266)
k_ras = (0, -0.322266, 0.946649)
writing to 002/tmp.mc-afni2.21157/invol.nii.gz...
#@# --------------------------------
/expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold
3dvolreg.afni -verbose -dfile 002/fmcpr.mcdat -1Dmatrix_save 002/fmcpr.mat -base 002/tmp.mc-afni2.21157/tempvol.nii.gz -prefix 002/tmp.mc-afni2.21157/outvol.nii.gz 002/tmp.mc-afni2.21157/invol.nii.gz
++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit]
++ Authored by: RW Cox
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as 002/tmp.mc-afni2.21157/tempvol.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:002/tmp.mc-afni2.21157/tempvol.nii.gz is 18.799990 degrees from plumb.
++ Reading in base dataset 002/tmp.mc-afni2.21157/tempvol.nii.gz
++ Oblique dataset:002/tmp.mc-afni2.21157/invol.nii.gz is 18.799990 degrees from plumb.
++ Reading input dataset 002/tmp.mc-afni2.21157/invol.nii.gz
++ Edging: x=3 y=3 z=2
++ Creating mask for -maxdisp
+ Automask has 55699 voxels
+ 7724 voxels left in -maxdisp mask after erosion
++ Initializing alignment base
++ Starting final pass on 360 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237..238..239..240..241..242..243..244..245..246..247..248..249..250..251..252..253..254..255..256..257..258..259..260..261..262..263..264..265..266..267..268..269..270..271..272..273..274..275..276..277..278..279..280..281..282..283..284..285..286..287..288..289..290..291..292..293..294..295..296..297..298..299..300..301..302..303..304..305..306..307..308..309..310..311..312..313..314..315..316..317..318..319..320..321..322..323..324..325..326..327..328..329..330..331..332..333..334..335..336..337..338..339..340..341..342..343..344..345..346..347..348..349..350..351..352..353..354..355..356..357..358..359..
++ CPU time for realignment=0 s [=0 s/sub-brick]
++ Min : roll=-0.118 pitch=-1.217 yaw=-0.225 dS=-0.601 dL=-0.394 dP=-0.185
++ Mean: roll=+0.020 pitch=-0.177 yaw=-0.055 dS=-0.097 dL=-0.042 dP=+0.235
++ Max : roll=+0.197 pitch=+0.404 yaw=+0.051 dS=+0.947 dL=+0.210 dP=+1.071
++ Max displacements (mm) for each sub-brick:
1.72 1.45 1.25 1.22 1.08 1.07 1.20 0.97 0.84 0.77 0.89 0.77 0.79 0.50 0.56 0.58 0.53 0.42 0.51 0.61 0.68 0.54 0.55 0.42 0.42 0.33 0.38 0.33 0.35 0.30 0.30 0.27 0.30 0.27 0.37 0.22 0.57 0.32 0.32 0.38 0.28 0.66 0.58 0.54 0.53 0.51 0.38 0.45 0.37 0.28 0.23 0.28 0.29 0.52 0.35 0.38 0.48 0.25 0.29 0.33 0.32 0.37 0.43 0.39 0.51 0.57 0.39 0.45 0.47 0.68 0.90 0.74 0.78 0.55 0.58 0.65 1.17 1.00 0.58 0.50 0.88 0.75 0.69 0.65 0.45 0.44 0.46 0.28 0.22 0.36 0.25 0.29 0.36 0.55 0.50 0.35 0.34 0.49 0.34 0.37 0.54 0.60 0.72 0.31 0.30 0.28 0.34 0.43 0.46 0.33 0.47 0.35 0.50 0.50 0.51 0.57 0.62 0.54 0.51 0.57 0.45 0.47 0.51 0.52 0.37 0.32 0.37 0.29 0.26 0.34 0.35 0.34 0.42 0.51 0.46 0.41 0.34 0.27 0.27 0.15 0.21 0.26 0.10 0.10 0.08 0.09 0.17 0.13 0.10 0.11 0.15 0.10 0.12 0.10 0.21 0.17 0.16 0.17 0.17 0.20 0.22 0.15 0.17 0.15 0.19 0.14 0.15 0.15 0.17 0.24 0.18 0.23 0.25 0.25 0.26 0.25 0.31 0.25 0.15 0.12 0.00 0.07 0.11 0.08 0.07 0.17 0.29 0.18 0.16 0.16 0.15 0.17 0.14 0.18 0.27 0.25 0.17 0.19 0.16 0.18 0.41 0.33 0.29 0.34 0.37 0.37 0.39 0.39 0.39 0.39 0.32 0.24 0.26 0.22 0.21 0.20 0.21 0.17 0.22 0.46 0.25 0.42 0.32 0.28 0.30 0.23 0.20 0.29 0.27 0.32 0.30 0.19 0.24 0.25 0.47 0.45 0.43 0.35 0.29 0.29 0.32 0.32 0.31 0.32 0.32 0.33 0.37 0.29 0.30 0.29 0.26 0.29 0.48 0.45 0.52 0.81 0.59 0.59 0.62 0.59 0.53 0.58 0.61 0.64 0.63 0.61 0.61 0.63 0.66 0.62 0.75 0.81 0.86 0.97 0.94 0.94 0.87 0.89 0.92 0.91 0.91 0.91 0.94 0.84 0.85 0.86 0.83 0.98 0.99 0.99 1.01 0.92 1.00 1.07 1.23 1.42 1.44 1.60 1.53 1.61 1.65 1.68 1.74 1.78 1.79 1.75 1.68 1.79 1.85 1.49 1.65 1.74 1.70 1.79 1.76 1.41 1.46 1.56 1.60 1.61 1.62 1.65 1.61 1.69 1.48 1.74 1.82 1.83 1.79 1.77 1.84 1.86 1.88 1.87 1.70 1.77 1.88 1.98 1.90 1.82 1.77 1.83 1.84 1.89 1.92 1.97 2.03 2.06 2.13 2.11 2.19 2.17 2.23 2.24 2.18 2.18 2.28 2.19 2.15 2.35
++ Max displacement in automask = 2.35 (mm) at sub-brick 359
++ Wrote dataset to disk in 002/tmp.mc-afni2.21157/outvol.nii.gz
#@# --------------------------------
/expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold
mri_convert 002/tmp.mc-afni2.21157/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii.gz
mri_convert.bin 002/tmp.mc-afni2.21157/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii.gz
reading info from 002/template.nii.gz...
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from 002/tmp.mc-afni2.21157/outvol.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
INFO: frames are not the same
i_ras = (-1, 0, 0)
j_ras = (0, 0.946649, 0.322266)
k_ras = (0, -0.322266, 0.946649)
writing to 002/fmcpr.nii.gz...
... cleaning up ....
Sun Feb 11 14:20:46 PST 2018
mc-afni2 done
INFO: Making external regressor from mc params
mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg
Sun Feb 11 14:20:46 PST 2018
setenv SUBJECTS_DIR /opt/fmritools/freesurfer/subjects
cd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold
/opt/fmritools/freesurfer/fsfast/bin/mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux msm2 4.12.0-1-amd64 #1 SMP Debian 4.12.6-1 (2017-08-12) x86_64 GNU/Linux
mri_glmfit --table /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/table.dat --glmdir /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/glm --osgm --y-out /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/y.out.nii --pca
$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold
cmdline mri_glmfit.bin --table /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/table.dat --glmdir /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/glm --osgm --y-out /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/y.out.nii --pca
sysname Linux
hostname msm2
machine x86_64
user bensmith
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/table.dat
logyflag 0
usedti 0
glmdir /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/glm
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/glm
Loading y from /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/table.dat
Found 6 data colums
Found 360 data rows
Saving design matrix to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/glm/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1
search space = 6.000000
DOF = 359
Starting fit and test
Fit completed in 1.66667e-05 minutes
Writing results
osgm
maxvox sig=-1e+10 F=676.016 at index 2 0 0 seed=1519356491
Measure:MC osgm
Tx 10.001
Ty -16.531
Tz -10000000000.000
Rx -13.508
Ry -13.109
Rz 34.326
Computing PCA (360)
mri_glmfit done
ninputs = 1
Checking inputs
nframestot = 360
Allocing output
Done allocing
nframes = 360
Computing PCA
Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/pca.nii
mcdat2mcextreg done
Sun Feb 11 14:20:48 PST 2018
mc-sess completed SUCCESSFULLY
sub106sess To Surface -----------------------------
rawfunc2surf-sess -fwhm 5 -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -fsd bold -trgsubject fsaverage -update -per-run
instem fmcpr
outstem fmcpr.sm5.fsaverage.hemi
------------------------------
1/1 sub106sess
1/1 sub106sess 001 lh ---------
Sun Feb 11 14:20:48 PST 2018
mri_vol2surf --mov /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.nii.gz --reg /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg
srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.nii.gz
srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Input reg is LTA
-------- original matrix -----------
1.00000 0.00076 -0.00217 -2.58076;
0.00226 -0.16210 0.98677 -9.17842;
0.00040 -0.98677 -0.16211 1.60844;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Loading label /opt/fmritools/freesurfer/subjects/fsaverage/label/lh.cortex.label
Reading surface /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.white
Done reading source surface
Reading thickness /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 14848
Reading source surface registration
/opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.sphere.reg
Done loading source registration surface
Reading target registration
/opt/fmritools/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
Done loading target registration surface
Mapping Surfaces (msm20171025T154741sub106 -> fsaverage)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (153634)
Reverse Loop had 30979 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
Done mapping surfaces
nSrc121 = 120220, nSrcLost = 0, nSrcMulti = 33414, MnSrcMultiHits = 2.23263
nTrg121 = 140149, nTrgMulti = 23693, MnTrgMultiHits = 2.30752
Masking with /opt/fmritools/freesurfer/subjects/fsaverage/label/lh.cortex.label
Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz
Dim: 163842 1 1
mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed
cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz
sysname Linux
hostname msm2
machine x86_64
user bensmith
input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz
Binarizing based on threshold
min 1e-05
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 149949 values in range
Counting number of voxels in first frame
Found 149949 voxels in final mask
Count: 149949 149949.000000 163842 91.520489
mri_binarize done
1/1 sub106sess 002 lh ---------
Sun Feb 11 14:20:56 PST 2018
mri_vol2surf --mov /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.nii.gz --reg /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg
srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.nii.gz
srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/register.dof6.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Input reg is LTA
-------- original matrix -----------
0.99805 -0.06220 -0.00581 -7.94137;
-0.01829 -0.37984 0.92487 -14.76863;
-0.05973 -0.92296 -0.38023 -8.59879;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Loading label /opt/fmritools/freesurfer/subjects/fsaverage/label/lh.cortex.label
Reading surface /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.white
Done reading source surface
Reading thickness /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 14645
Reading source surface registration
/opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.sphere.reg
Done loading source registration surface
Reading target registration
/opt/fmritools/freesurfer/subjects/fsaverage/surf/lh.sphere.reg
Done loading target registration surface
Mapping Surfaces (msm20171025T154741sub106 -> fsaverage)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (153634)
Reverse Loop had 30979 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
Done mapping surfaces
nSrc121 = 120220, nSrcLost = 0, nSrcMulti = 33414, MnSrcMultiHits = 2.23263
nTrg121 = 140149, nTrgMulti = 23693, MnTrgMultiHits = 2.30752
Masking with /opt/fmritools/freesurfer/subjects/fsaverage/label/lh.cortex.label
Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz
Dim: 163842 1 1
mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed
cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz
sysname Linux
hostname msm2
machine x86_64
user bensmith
input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz
Binarizing based on threshold
min 1e-05
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 149298 values in range
Counting number of voxels in first frame
Found 149298 voxels in final mask
Count: 149298 149298.000000 163842 91.123155
mri_binarize done
mri_concat --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz --mean /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Computing mean across frames
Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz
mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz --min 10e-10 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed
cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz --min 10e-10 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz
sysname Linux
hostname msm2
machine x86_64
user bensmith
input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz
Binarizing based on threshold
min 1e-09
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 149949 values in range
Counting number of voxels in first frame
Found 149949 voxels in final mask
Count: 149949 149949.000000 163842 91.520489
mri_binarize done
1/1 sub106sess 001 rh ---------
Sun Feb 11 14:21:04 PST 2018
mri_vol2surf --mov /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.nii.gz --reg /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg
srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.nii.gz
srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Input reg is LTA
-------- original matrix -----------
1.00000 0.00076 -0.00217 -2.58076;
0.00226 -0.16210 0.98677 -9.17842;
0.00040 -0.98677 -0.16211 1.60844;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Loading label /opt/fmritools/freesurfer/subjects/fsaverage/label/rh.cortex.label
Reading surface /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.white
Done reading source surface
Reading thickness /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 14509
Reading source surface registration
/opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.sphere.reg
Done loading source registration surface
Reading target registration
/opt/fmritools/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Done loading target registration surface
Mapping Surfaces (msm20171025T154741sub106 -> fsaverage)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (151643)
Reverse Loop had 30576 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
Done mapping surfaces
nSrc121 = 117501, nSrcLost = 0, nSrcMulti = 34142, MnSrcMultiHits = 2.25286
nTrg121 = 140913, nTrgMulti = 22929, MnTrgMultiHits = 2.33351
Masking with /opt/fmritools/freesurfer/subjects/fsaverage/label/rh.cortex.label
Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz
Dim: 163842 1 1
mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed
cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz
sysname Linux
hostname msm2
machine x86_64
user bensmith
input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz
Binarizing based on threshold
min 1e-05
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 149917 values in range
Counting number of voxels in first frame
Found 149917 voxels in final mask
Count: 149917 149917.000000 163842 91.500958
mri_binarize done
1/1 sub106sess 002 rh ---------
Sun Feb 11 14:21:12 PST 2018
mri_vol2surf --mov /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.nii.gz --reg /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg
srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.nii.gz
srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/register.dof6.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Input reg is LTA
-------- original matrix -----------
0.99805 -0.06220 -0.00581 -7.94137;
-0.01829 -0.37984 0.92487 -14.76863;
-0.05973 -0.92296 -0.38023 -8.59879;
0.00000 0.00000 0.00000 1.00000;
-------- original matrix -----------
Loading label /opt/fmritools/freesurfer/subjects/fsaverage/label/rh.cortex.label
Reading surface /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.white
Done reading source surface
Reading thickness /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.5 0.5 0.5
using old
Done mapping volume to surface
Number of source voxels hit = 14335
Reading source surface registration
/opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.sphere.reg
Done loading source registration surface
Reading target registration
/opt/fmritools/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Done loading target registration surface
Mapping Surfaces (msm20171025T154741sub106 -> fsaverage)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (151643)
Reverse Loop had 30576 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
Done mapping surfaces
nSrc121 = 117501, nSrcLost = 0, nSrcMulti = 34142, MnSrcMultiHits = 2.25286
nTrg121 = 140913, nTrgMulti = 22929, MnTrgMultiHits = 2.33351
Masking with /opt/fmritools/freesurfer/subjects/fsaverage/label/rh.cortex.label
Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz
Dim: 163842 1 1
mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed
cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz
sysname Linux
hostname msm2
machine x86_64
user bensmith
input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz
Binarizing based on threshold
min 1e-05
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 148821 values in range
Counting number of voxels in first frame
Found 148821 voxels in final mask
Count: 148821 148821.000000 163842 90.832021
mri_binarize done
mri_concat --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz --mean /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Computing mean across frames
Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz
mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz --min 10e-10 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz
$Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $
cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed
cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz --min 10e-10 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz
sysname Linux
hostname msm2
machine x86_64
user bensmith
input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz
frame 0
nErode3d 0
nErode2d 0
output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz
Binarizing based on threshold
min 1e-09
max +infinity
binval 1
binvalnot 0
fstart = 0, fend = 0, nframes = 1
Found 149917 values in range
Counting number of voxels in first frame
Found 149917 voxels in final mask
Count: 149917 149917.000000 163842 91.500958
mri_binarize done
1/1 sub106sess 001 lh ---------
Sun Feb 11 14:21:20 PST 2018
mri_vol2surf --mov /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz --reg /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg
niiRead(): error reading from /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz
srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz
srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = fsaverage
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
reshape = 0
interp = trilin
float2int = round
GetProjMax = 0
INFO: float2int code = 0
ERROR: Read 13, expected 64
ERROR: could not read /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz as type 24
_______________________
Ben Smith, MSc.
Ph.D. Candidate
University of Southern California
w | +1 213-740 7851
m | +1 323-385 9349