Log file for vlrmerge Tue Sep 10 18:44:12 EDT 2019 setenv SUBJECTS_DIR /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects cd /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group /media/sda1/nmrclass/freesurfer/fsfast/bin/vlrmerge --o encode.merged.nii.gz --lh workmem.sm05.lh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz --rh workmem.sm05.rh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz --vol workmem.sm05.mni305/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz --scm workmem.sm05.mni305/subcort.mask.nii.gz $Id: vlrmerge,v 1.5 2015/12/10 22:51:31 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-tutorial-2beb96c Linux fsuser3-G5-5587 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux mri_surf2vol --fstal 2 --template /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsaverage/mri.2mm/orig.mgz --hemi lh --surfval workmem.sm05.lh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz --o /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh --fillribbon gdiagno = -1 Qa2v: SurfXYZ to VolCRS: ------------------------------ -0.50000 0.00000 0.00000 37.00000; 0.00000 0.00000 -0.50000 42.50000; 0.00000 0.50000 0.00000 54.50000; 0.00000 0.00000 0.00000 1.00000; -------------------------------------------------- subjects dir /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects surface value path workmem.sm05.lh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz hemi lh mksurfmask 0 projfrac 0 volreg file /media/sda1/nmrclass/freesurfer/average/mni305.cor.subfov2.reg outvol path /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh template path /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsaverage/mri.2mm/orig.mgz ------- Anat2Vol Registration (TkReg)---- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; ----------------------------------------- height = 76 width = 76 depth = 93 xsize = 2.000000 ysize = 2.000000 zsize = 2.000000 cdc = -1.000000 0.000000 0.000000 rdc = 0.000000 0.000000 -1.000000 sdc = 0.000000 1.000000 0.000000 xyz0 = -2.000000 -16.000000 9.000000 Gdiag_no -1 Reading surface /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.white Done reading source surface Reading thickness /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/lh.thickness Done INFO: reading workmem.sm05.lh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz as nii Done loading source values (nvtxs = 163842) INFO: mapping vertices to closest voxel VtxVol fixed INFO: resampling surface to volume at projfrac=0.00, 21476 hits INFO: resampling surface to volume at projfrac=0.05, 21580 hits INFO: resampling surface to volume at projfrac=0.10, 21696 hits INFO: resampling surface to volume at projfrac=0.15, 21875 hits INFO: resampling surface to volume at projfrac=0.20, 21987 hits INFO: resampling surface to volume at projfrac=0.25, 22138 hits INFO: resampling surface to volume at projfrac=0.30, 22194 hits INFO: resampling surface to volume at projfrac=0.35, 22333 hits INFO: resampling surface to volume at projfrac=0.40, 22500 hits INFO: resampling surface to volume at projfrac=0.45, 22588 hits INFO: resampling surface to volume at projfrac=0.50, 22699 hits INFO: resampling surface to volume at projfrac=0.55, 22834 hits INFO: resampling surface to volume at projfrac=0.60, 22948 hits INFO: resampling surface to volume at projfrac=0.65, 23004 hits INFO: resampling surface to volume at projfrac=0.70, 23098 hits INFO: resampling surface to volume at projfrac=0.75, 23201 hits INFO: resampling surface to volume at projfrac=0.80, 23292 hits INFO: resampling surface to volume at projfrac=0.85, 23375 hits INFO: resampling surface to volume at projfrac=0.90, 23435 hits INFO: resampling surface to volume at projfrac=0.95, 23512 hits INFO: writing output volume to /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh done mri_surf2vol --fstal 2 --merge /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh --hemi rh --surfval workmem.sm05.rh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz --o /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh --fillribbon gdiagno = -1 Using merge volume as template Qa2v: SurfXYZ to VolCRS: ------------------------------ -0.50000 0.00000 0.00000 37.00000; 0.00000 0.00000 -0.50000 42.50000; 0.00000 0.50000 0.00000 54.50000; 0.00000 0.00000 0.00000 1.00000; -------------------------------------------------- subjects dir /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects surface value path workmem.sm05.rh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz hemi rh mksurfmask 0 projfrac 0 volreg file /media/sda1/nmrclass/freesurfer/average/mni305.cor.subfov2.reg outvol path /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh template path /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh ------- Anat2Vol Registration (TkReg)---- 1.00000 0.00000 0.00000 2.00000; 0.00000 1.00000 0.00000 16.00000; 0.00000 0.00000 1.00000 -9.00000; 0.00000 0.00000 0.00000 1.00000; ----------------------------------------- height = 76 width = 76 depth = 93 xsize = 2.000000 ysize = 2.000000 zsize = 2.000000 cdc = -1.000000 0.000000 0.000000 rdc = 0.000000 0.000000 -1.000000 sdc = 0.000000 1.000000 0.000000 xyz0 = -2.000000 -16.000000 9.000000 Gdiag_no -1 Reading surface /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/rh.white Done reading source surface Reading thickness /media/sda1/nmrclass/tutorial_data/fsfast-tutorial.subjects/fsaverage/surf/rh.thickness Done INFO: reading workmem.sm05.rh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz as nii Done loading source values (nvtxs = 163842) INFO: mapping vertices to closest voxel VtxVol fixed INFO: resampling surface to volume at projfrac=0.00, 21221 hits INFO: resampling surface to volume at projfrac=0.05, 21425 hits INFO: resampling surface to volume at projfrac=0.10, 21538 hits INFO: resampling surface to volume at projfrac=0.15, 21727 hits INFO: resampling surface to volume at projfrac=0.20, 21779 hits INFO: resampling surface to volume at projfrac=0.25, 21890 hits INFO: resampling surface to volume at projfrac=0.30, 22059 hits INFO: resampling surface to volume at projfrac=0.35, 22232 hits INFO: resampling surface to volume at projfrac=0.40, 22305 hits INFO: resampling surface to volume at projfrac=0.45, 22427 hits INFO: resampling surface to volume at projfrac=0.50, 22587 hits INFO: resampling surface to volume at projfrac=0.55, 22585 hits INFO: resampling surface to volume at projfrac=0.60, 22701 hits INFO: resampling surface to volume at projfrac=0.65, 22878 hits INFO: resampling surface to volume at projfrac=0.70, 22937 hits INFO: resampling surface to volume at projfrac=0.75, 23010 hits INFO: resampling surface to volume at projfrac=0.80, 23077 hits INFO: resampling surface to volume at projfrac=0.85, 23180 hits INFO: resampling surface to volume at projfrac=0.90, 23282 hits INFO: resampling surface to volume at projfrac=0.95, 23478 hits INFO: writing output volume to /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh done mri_binarize --min 0.5 --i workmem.sm05.mni305/subcort.mask.nii.gz --inv --o /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/subcortmaskinv.nii $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group cmdline mri_binarize.bin --min 0.5 --i workmem.sm05.mni305/subcort.mask.nii.gz --inv --o /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/subcortmaskinv.nii sysname Linux hostname fsuser3-G5-5587 machine x86_64 user nmrclass input workmem.sm05.mni305/subcort.mask.nii.gz frame 0 nErode3d 0 nErode2d 0 output /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/subcortmaskinv.nii Binarizing based on threshold min 0.5 max +infinity binval 0 binvalnot 1 fstart = 0, fend = 0, nframes = 1 Found 51000 values in range Counting number of voxels in first frame Found 51000 voxels in final mask Count: 51000 408000.000000 537168 9.494236 mri_binarize done mri_mask /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/subcortmaskinv.nii /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh DoAbs = 0 Writing masked volume to /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh...done. mri_mask workmem.sm05.mni305/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz workmem.sm05.mni305/subcort.mask.nii.gz /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/involmasked.nii DoAbs = 0 Writing masked volume to /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/involmasked.nii...done. mri_concat --sum /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/junk.mgh /media/sda1/nmrclass/tutorial_data_Sep_2019_rev3/fsfast-functional/group/tmpdir.vlrmerge/involmasked.nii --o encode.merged.nii.gz ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Computing sum across frames Writing to encode.merged.nii.gz Tue Sep 10 18:44:16 EDT 2019 vlrmerge done