probably fmcpr.nii.gz got corrupted. Did you run out of disk space?
On 2/11/18 6:07 PM, Ben Smith wrote:
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 https://bjsmith.github.io/ w | +1 213-740 7851 m | +1 323-385 9349 skype | ben.smith.nz http://ben.smith.nz/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer