Hi All, I'm running into an error analyzing some fMRI data with FS-FAST in Freesurfer version 5.3. The analysis runs fine until it gets to the register-sess part, which quits before actually starting to do any registration. The last line of the log file, attached, is "if: Expression syntax", but there are no other errors prior to that. The command I'm using, analysis, and contrasts have all worked on several other similar data sets. Has anyone encountered this problem before, or know what's causing it?
Thanks, Matt Clinical Research Coordinator Stufflebeam Lab Athinoula A. Martinos Center Massachusetts General Hospital 149 13th Street, Room 1115S Charlestown, MA 02129
selxavg3-sess log file /usr/local/freesurfer/stable5_3_0/fsfast/bin/selxavg3-sess -analysis sycabs_self_lh -s nmr00978 -d /cluster/neuromind/dwakeman/tsc_pilot/subjects/ $Id: selxavg3-sess,v 1.57.2.1 2011/12/09 20:06:47 greve Exp $ uid=3882345(kz221) gid=3882345(kz221) groups=3882345(kz221),1084(megclin),1125(smsgp) /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed Jul 13 13:42:24 EDT 2016 preproc-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -a sycabs_self_lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ kz221 setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/ Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -a sycabs_self_lh -nolog Wed Jul 13 13:42:25 EDT 2016 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain nmr00978 Template ----------------------------- mktemplate-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -nolog -update Session: /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ---------------- Wed Jul 13 13:42:25 EDT 2016 Detected input format at nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/template.nii.gz --frame 0 mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/template.nii.gz --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.0077173, -0.178789, 0.983857) keeping frame 0 writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/template.nii.gz... Run: 009 ---------------- Wed Jul 13 13:42:36 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/template.nii.gz --mid-frame mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/f.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.0077173, -0.178789, 0.983857) keeping frame 238 writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/template.nii.gz... Run: 010 ---------------- Wed Jul 13 13:42:46 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/template.nii.gz --mid-frame mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/f.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.0077173, -0.178789, 0.983857) keeping frame 238 writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/template.nii.gz... Run: 011 ---------------- Wed Jul 13 13:42:56 EDT 2016 /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/template.nii.gz --mid-frame mri_convert /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/f.nii.gz /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/template.nii.gz --mid-frame $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/f.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.0077173, -0.178789, 0.983857) keeping frame 238 writing to /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/template.nii.gz... Wed Jul 13 13:43:06 EDT 2016 mktemplate-sess completed nmr00978 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd sycabs -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -nolog -update ------------------------------------------------ /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 Wed Jul 13 13:43:06 EDT 2016 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_31088 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_convert template.nii.gz /tmp/mkbrainmask_31088/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_31088/in.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from template.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.00771731, -0.178789, 0.983857) writing to /tmp/mkbrainmask_31088/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs bet.fsl /tmp/mkbrainmask_31088/in.nii /tmp/mkbrainmask_31088/brain -m -f 0.1 mri_binarize --i /tmp/mkbrainmask_31088/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31088/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i /tmp/mkbrainmask_31088/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31088/brain_mask.nii sysname Linux hostname belle machine x86_64 user kz221 input /tmp/mkbrainmask_31088/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_31088/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 Found 93758 values in range Counting number of voxels Found 93758 voxels in final mask mri_binarize done Diliating 1 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_binarize --i /tmp/mkbrainmask_31088/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31088/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i /tmp/mkbrainmask_31088/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31088/brain_mask.nii sysname Linux hostname belle machine x86_64 user kz221 input /tmp/mkbrainmask_31088/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_31088/brain_mask.nii Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 93758 values in range Dilating 1 voxels in 3d Counting number of voxels Found 108842 voxels in final mask mri_binarize done /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_convert /tmp/mkbrainmask_31088/brain_mask.nii masks/brain.nii.gz mri_convert /tmp/mkbrainmask_31088/brain_mask.nii masks/brain.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /tmp/mkbrainmask_31088/brain_mask.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.00771731, -0.178789, 0.983857) writing to masks/brain.nii.gz... ----------------- mkbrainmask Done ----------------------------- mkbrainmask -i 009/template.nii.gz -o 009/masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_31202 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_convert 009/template.nii.gz /tmp/mkbrainmask_31202/in.nii mri_convert 009/template.nii.gz /tmp/mkbrainmask_31202/in.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 009/template.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.00771731, -0.178789, 0.983857) writing to /tmp/mkbrainmask_31202/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs bet.fsl /tmp/mkbrainmask_31202/in.nii /tmp/mkbrainmask_31202/brain -m -f 0.1 mri_binarize --i /tmp/mkbrainmask_31202/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31202/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i /tmp/mkbrainmask_31202/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31202/brain_mask.nii sysname Linux hostname belle machine x86_64 user kz221 input /tmp/mkbrainmask_31202/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_31202/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 Found 97811 values in range Counting number of voxels Found 97811 voxels in final mask mri_binarize done Diliating 1 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_binarize --i /tmp/mkbrainmask_31202/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31202/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i /tmp/mkbrainmask_31202/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31202/brain_mask.nii sysname Linux hostname belle machine x86_64 user kz221 input /tmp/mkbrainmask_31202/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_31202/brain_mask.nii Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 97811 values in range Dilating 1 voxels in 3d Counting number of voxels Found 113218 voxels in final mask mri_binarize done /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_convert /tmp/mkbrainmask_31202/brain_mask.nii 009/masks/brain.nii.gz mri_convert /tmp/mkbrainmask_31202/brain_mask.nii 009/masks/brain.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /tmp/mkbrainmask_31202/brain_mask.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.00771731, -0.178789, 0.983857) writing to 009/masks/brain.nii.gz... ----------------- mkbrainmask Done ----------------------------- mri_binarize --i 009/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 009/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i 009/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 009/masks/brain.e3.nii.gz sysname Linux hostname belle machine x86_64 user kz221 input 009/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 009/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 110421 values in range Eroding 3 voxels in 3d Counting number of voxels Found 66091 voxels in final mask mri_binarize done meanval --i 009/f.nii.gz --m 009/masks/brain.e3.nii.gz --o 009/global.meanval.dat --avgwf 009/global.waveform.dat Wed Jul 13 13:43:10 EDT 2016 setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/ cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs /usr/local/freesurfer/stable5_3_0/bin/meanval --i 009/f.nii.gz --m 009/masks/brain.e3.nii.gz --o 009/global.meanval.dat --avgwf 009/global.waveform.dat cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 009/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/tmpdir.meanval.31316/blah.31316 --in 009/f.nii.gz --sfavg 009/global.meanval.dat --avgwf 009/global.waveform.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg 009/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/009/tmpdir.meanval.31316/blah.31316 --in 009/f.nii.gz --sfavg 009/global.meanval.dat --avgwf 009/global.waveform.dat sysname Linux hostname belle machine x86_64 user kz221 UseRobust 0 Loading 009/masks/brain.e3.nii.gz Loading 009/f.nii.gz Voxel Volume is 27 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 66091 1784457.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to 009/global.meanval.dat 0 442.671 Writing to 009/global.waveform.dat mri_segstats done mkbrainmask -i 010/template.nii.gz -o 010/masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_31412 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_convert 010/template.nii.gz /tmp/mkbrainmask_31412/in.nii mri_convert 010/template.nii.gz /tmp/mkbrainmask_31412/in.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 010/template.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.00771731, -0.178789, 0.983857) writing to /tmp/mkbrainmask_31412/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs bet.fsl /tmp/mkbrainmask_31412/in.nii /tmp/mkbrainmask_31412/brain -m -f 0.1 mri_binarize --i /tmp/mkbrainmask_31412/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31412/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i /tmp/mkbrainmask_31412/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31412/brain_mask.nii sysname Linux hostname belle machine x86_64 user kz221 input /tmp/mkbrainmask_31412/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_31412/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 Found 87365 values in range Counting number of voxels Found 87365 voxels in final mask mri_binarize done Diliating 1 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_binarize --i /tmp/mkbrainmask_31412/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31412/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i /tmp/mkbrainmask_31412/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31412/brain_mask.nii sysname Linux hostname belle machine x86_64 user kz221 input /tmp/mkbrainmask_31412/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_31412/brain_mask.nii Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 87365 values in range Dilating 1 voxels in 3d Counting number of voxels Found 102420 voxels in final mask mri_binarize done /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_convert /tmp/mkbrainmask_31412/brain_mask.nii 010/masks/brain.nii.gz mri_convert /tmp/mkbrainmask_31412/brain_mask.nii 010/masks/brain.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /tmp/mkbrainmask_31412/brain_mask.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.00771731, -0.178789, 0.983857) writing to 010/masks/brain.nii.gz... ----------------- mkbrainmask Done ----------------------------- mri_binarize --i 010/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 010/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i 010/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 010/masks/brain.e3.nii.gz sysname Linux hostname belle machine x86_64 user kz221 input 010/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 010/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 100377 values in range Eroding 3 voxels in 3d Counting number of voxels Found 58222 voxels in final mask mri_binarize done meanval --i 010/f.nii.gz --m 010/masks/brain.e3.nii.gz --o 010/global.meanval.dat --avgwf 010/global.waveform.dat Wed Jul 13 13:43:24 EDT 2016 setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/ cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs /usr/local/freesurfer/stable5_3_0/bin/meanval --i 010/f.nii.gz --m 010/masks/brain.e3.nii.gz --o 010/global.meanval.dat --avgwf 010/global.waveform.dat cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 010/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/tmpdir.meanval.31526/blah.31526 --in 010/f.nii.gz --sfavg 010/global.meanval.dat --avgwf 010/global.waveform.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg 010/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/010/tmpdir.meanval.31526/blah.31526 --in 010/f.nii.gz --sfavg 010/global.meanval.dat --avgwf 010/global.waveform.dat sysname Linux hostname belle machine x86_64 user kz221 UseRobust 0 Loading 010/masks/brain.e3.nii.gz Loading 010/f.nii.gz Voxel Volume is 27 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 58222 1571994.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to 010/global.meanval.dat 0 472.463 Writing to 010/global.waveform.dat mri_segstats done mkbrainmask -i 011/template.nii.gz -o 011/masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHS fslmaths.fsl Scratch Dir is /tmp/mkbrainmask_31629 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_convert 011/template.nii.gz /tmp/mkbrainmask_31629/in.nii mri_convert 011/template.nii.gz /tmp/mkbrainmask_31629/in.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from 011/template.nii.gz... TR=568.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.00771731, -0.178789, 0.983857) writing to /tmp/mkbrainmask_31629/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs bet.fsl /tmp/mkbrainmask_31629/in.nii /tmp/mkbrainmask_31629/brain -m -f 0.1 mri_binarize --i /tmp/mkbrainmask_31629/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31629/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i /tmp/mkbrainmask_31629/brain_mask.nii --min .01 --o /tmp/mkbrainmask_31629/brain_mask.nii sysname Linux hostname belle machine x86_64 user kz221 input /tmp/mkbrainmask_31629/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_31629/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 Found 87486 values in range Counting number of voxels Found 87486 voxels in final mask mri_binarize done Diliating 1 /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_binarize --i /tmp/mkbrainmask_31629/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31629/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i /tmp/mkbrainmask_31629/brain_mask.nii --min 0.5 --dilate 1 --o /tmp/mkbrainmask_31629/brain_mask.nii sysname Linux hostname belle machine x86_64 user kz221 input /tmp/mkbrainmask_31629/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_31629/brain_mask.nii Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 87486 values in range Dilating 1 voxels in 3d Counting number of voxels Found 102213 voxels in final mask mri_binarize done /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs mri_convert /tmp/mkbrainmask_31629/brain_mask.nii 011/masks/brain.nii.gz mri_convert /tmp/mkbrainmask_31629/brain_mask.nii 011/masks/brain.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /tmp/mkbrainmask_31629/brain_mask.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99997, -0.00137983, 0.00759295) j_ras = (1.9297e-08, -0.983886, -0.178794) k_ras = (0.00771731, -0.178789, 0.983857) writing to 011/masks/brain.nii.gz... ----------------- mkbrainmask Done ----------------------------- mri_binarize --i 011/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 011/masks/brain.e3.nii.gz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs cmdline mri_binarize --i 011/masks/brain.nii.gz --min 0.5 --zero-edges --erode 3 --o 011/masks/brain.e3.nii.gz sysname Linux hostname belle machine x86_64 user kz221 input 011/masks/brain.nii.gz frame 0 nErode3d 3 nErode2d 0 output 011/masks/brain.e3.nii.gz Binarizing based on threshold min 0.5 max +infinity binval 1 binvalnot 0 Found 99973 values in range Eroding 3 voxels in 3d Counting number of voxels Found 58324 voxels in final mask mri_binarize done meanval --i 011/f.nii.gz --m 011/masks/brain.e3.nii.gz --o 011/global.meanval.dat --avgwf 011/global.waveform.dat Wed Jul 13 13:43:36 EDT 2016 setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/ cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs /usr/local/freesurfer/stable5_3_0/bin/meanval --i 011/f.nii.gz --m 011/masks/brain.e3.nii.gz --o 011/global.meanval.dat --avgwf 011/global.waveform.dat cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux mri_segstats --seg 011/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/tmpdir.meanval.31733/blah.31733 --in 011/f.nii.gz --sfavg 011/global.meanval.dat --avgwf 011/global.waveform.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg 011/masks/brain.e3.nii.gz --id 1 --sum /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978/sycabs/011/tmpdir.meanval.31733/blah.31733 --in 011/f.nii.gz --sfavg 011/global.meanval.dat --avgwf 011/global.waveform.dat sysname Linux hostname belle machine x86_64 user kz221 UseRobust 0 Loading 011/masks/brain.e3.nii.gz Loading 011/f.nii.gz Voxel Volume is 27 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 58324 1574748.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to 011/global.meanval.dat 0 472.094 Writing to 011/global.waveform.dat mri_segstats done Wed Jul 13 13:43:47 EDT 2016 mkbrainmask-sess done nmr00978 Registration ----------------------------- register-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Wed Jul 13 13:43:48 EDT 2016 setenv SUBJECTS_DIR /cluster/neuromind/dwakeman/tsc_pilot/subjects/ cd /autofs/cluster/neuromind/dwakeman/tsc_pilot/fsfast /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s nmr00978 -d /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects -fsd sycabs -dof 6 -per-run -nolog -update cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory Linux belle 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Session: /autofs/cluster/neuromind/dwakeman/tsc_pilot/subjects/nmr00978 ---------------- Wed Jul 13 13:43:48 EDT 2016 if: Expression Syntax.
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