======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/denoised/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/step1/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/registration/t1_t2/affine.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/registration/t1_t2/warp.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/reslice/subject_t1/t2.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/denoised/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/step1/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/registration/t1_sri24_whole/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/registration/t1_sri24_whole/ants_1Warp.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/reslice/subject_t1/t1_sri24_whole/t1_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/reslice/subject_t1/t1_sri24_whole/t2_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/reslice/subject_t1/t1_sri24_whole/brainmask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/reslice/subject_t1/t1_sri24_whole/brainmask_10.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/denoised/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/step1/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/denoised/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/step1/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/robex_t1_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.OQJ36gyoG6 ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 1 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 9 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 3 seconds Step 4 of 9: calculating features...Done! It took roughly 17 seconds Step 5 of 9: voxel classification...Done! It took roughly 12 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 3 seconds Step 7 of 9: free deformation...Done! It took roughly 0 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 1 seconds Output ready The whole process took roughly 48 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/robex_t1b_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.06Uu0JTTwB ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 1 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 10 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 4 seconds Step 4 of 9: calculating features...Done! It took roughly 18 seconds Step 5 of 9: voxel classification...Done! It took roughly 12 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 1 seconds Step 7 of 9: free deformation...Done! It took roughly 1 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 0 seconds Output ready The whole process took roughly 49 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/bet_t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/bet_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/afni_t1_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/original/denoised/t1_masked.nii.gz -b /tmp/tmp.GXbbMdFX1U/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.GXbbMdFX1U/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/afni_t1b_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/step1/t1_masked.nii.gz -b /tmp/tmp.V99fOklNdw/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.V99fOklNdw/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/gcut_t1b_brain.nii.gz ======================================================================== error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale MRIchangeType: Building histogram 0 8322.18 1000, flo=0, fhi=0.999, dest_type=0 MRIchangeType: Building histogram 0 8322.18 1000, flo=0, fhi=0.999, dest_type=0 estimating WM mask white mean: 75.740915; seed number 360800 threshold set to: 75.740915*0.400000=30.296366 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale mri_convert --delete-cmds /tmp/tmp.rLKY0nDmFI/gcut_brain.mgz LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/gcut_t1b_brain.nii.gz reading from /tmp/tmp.rLKY0nDmFI/gcut_brain.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/gcut_t1b_brain.nii.gz... ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/gcut_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/bet_t2_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/bet_t2b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/afni_t2_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/original/denoised/t2_masked.nii.gz -b /tmp/tmp.2O4h0LoaY5/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.2O4h0LoaY5/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/afni_t2b_brain_mask.nii.gz ======================================================================== Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 84, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 96, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 108, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 120, avoid_vent -1 Warning 3dSkullStrip: Stubborn intersection remaining at smoothing of 120. Ignoring it.The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/step1/t2_masked.nii.gz -b /tmp/tmp.6I8xTE3Uey/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.6I8xTE3Uey/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/vote_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/voting/vote_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/step2/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/step2/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/step2/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/step2/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/t1_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/t1_skull.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/registration/t1_t2/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/denoised/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/mrbias/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/original/stripped/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/intensity_corrected/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/registration/t1_t2/affine.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/registration/t1_t2/warp.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/reslice/subject_t1/t2.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/denoised/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/step1/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/registration/t1_sri24_whole/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/registration/t1_sri24_whole/ants_1Warp.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/reslice/subject_t1/t1_sri24_whole/t1_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/reslice/subject_t1/t1_sri24_whole/t2_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/reslice/subject_t1/t1_sri24_whole/brainmask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/reslice/subject_t1/t1_sri24_whole/brainmask_10.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/denoised/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/step1/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/denoised/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/step1/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/robex_t1_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.94qoWfmJWh ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 1 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 9 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 3 seconds Step 4 of 9: calculating features...Done! It took roughly 19 seconds Step 5 of 9: voxel classification...Done! It took roughly 12 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 2 seconds Step 7 of 9: free deformation...Done! It took roughly 0 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 0 seconds Output ready The whole process took roughly 48 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/robex_t1b_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.tEzBtSdo5e ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 1 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 10 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 4 seconds Step 4 of 9: calculating features...Done! It took roughly 17 seconds Step 5 of 9: voxel classification...Done! It took roughly 12 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 2 seconds Step 7 of 9: free deformation...Done! It took roughly 0 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 1 seconds Output ready The whole process took roughly 49 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/bet_t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/bet_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/afni_t1_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/boosted/denoised/t1_masked.nii.gz -b /tmp/tmp.qHxEJNNLNq/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.qHxEJNNLNq/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/afni_t1b_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/step1/t1_masked.nii.gz -b /tmp/tmp.pvZmebw6Jn/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.pvZmebw6Jn/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/gcut_t1b_brain.nii.gz ======================================================================== error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale MRIchangeType: Building histogram 0 11016.9 1000, flo=0, fhi=0.999, dest_type=0 MRIchangeType: Building histogram 0 11016.9 1000, flo=0, fhi=0.999, dest_type=0 estimating WM mask white mean: 68.544115; seed number 437139 threshold set to: 68.544115*0.400000=27.417646 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale mri_convert --delete-cmds /tmp/tmp.qGXL6Ho2FS/gcut_brain.mgz LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/gcut_t1b_brain.nii.gz reading from /tmp/tmp.qGXL6Ho2FS/gcut_brain.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/gcut_t1b_brain.nii.gz... ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/gcut_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/bet_t2_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/bet_t2b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/afni_t2_brain_mask.nii.gz ======================================================================== Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 84, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 96, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 108, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 120, avoid_vent -1 Warning 3dSkullStrip: Stubborn intersection remaining at smoothing of 120. Ignoring it.The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/boosted/denoised/t2_masked.nii.gz -b /tmp/tmp.TF1q2IQYAb/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.TF1q2IQYAb/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/afni_t2b_brain_mask.nii.gz ======================================================================== Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 84, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 96, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 108, avoid_vent -1 The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/step1/t2_masked.nii.gz -b /tmp/tmp.NPZLrVPyUn/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.NPZLrVPyUn/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/vote_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/voting/vote_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/step2/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/step2/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/step2/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/step2/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/t1_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/t1_skull.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/registration/t1_t2/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/denoised/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/mrbias/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/boosted/stripped/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./denoised/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/step1/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/t1_t2/affine.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/t1_t2/warp.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/t2.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./denoised/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/step1/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/t1_sri24_whole/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/t1_sri24_whole/ants_1Warp.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/t1_sri24_whole/t1_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/t1_sri24_whole/t2_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/t1_sri24_whole/brainmask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/t1_sri24_whole/brainmask_10.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./denoised/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/step1/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./denoised/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/step1/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/robex_t1_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.SeCsDRMb4x ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 0 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 10 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 4 seconds Step 4 of 9: calculating features...Done! It took roughly 17 seconds Step 5 of 9: voxel classification...Done! It took roughly 12 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 3 seconds Step 7 of 9: free deformation...Done! It took roughly 0 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 1 seconds Output ready The whole process took roughly 49 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/robex_t1b_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.NyhkJb5V40 ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 0 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 10 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 5 seconds Step 4 of 9: calculating features...Done! It took roughly 18 seconds Step 5 of 9: voxel classification...Done! It took roughly 12 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 4 seconds Step 7 of 9: free deformation...Done! It took roughly 1 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 0 seconds Output ready The whole process took roughly 52 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/bet_t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/bet_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/afni_t1_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/./denoised/t1_masked.nii.gz -b /tmp/tmp.euITXuAAum/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.euITXuAAum/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/afni_t1b_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/step1/t1_masked.nii.gz -b /tmp/tmp.XIJVzGUP2D/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.XIJVzGUP2D/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/gcut_t1b_brain.nii.gz ======================================================================== error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale MRIchangeType: Building histogram 0 11016.9 1000, flo=0, fhi=0.999, dest_type=0 MRIchangeType: Building histogram 0 11016.9 1000, flo=0, fhi=0.999, dest_type=0 estimating WM mask white mean: 68.340201; seed number 439855 threshold set to: 68.340201*0.400000=27.336080 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale mri_convert --delete-cmds /tmp/tmp.ngus8kI3Ap/gcut_brain.mgz LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/gcut_t1b_brain.nii.gz reading from /tmp/tmp.ngus8kI3Ap/gcut_brain.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/gcut_t1b_brain.nii.gz... ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/gcut_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/bet_t2_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/bet_t2b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/afni_t2_brain_mask.nii.gz ======================================================================== Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 84, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 96, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 108, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 120, avoid_vent -1 Warning 3dSkullStrip: Stubborn intersection remaining at smoothing of 120. Ignoring it.The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/./denoised/t2_masked.nii.gz -b /tmp/tmp.TtSceP55Sd/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.TtSceP55Sd/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/afni_t2b_brain_mask.nii.gz ======================================================================== Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 84, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 96, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 108, avoid_vent -1 Warning 3dSkullStrip:**************** Surface self intersecting! trying again: smoothing of 120, avoid_vent -1 Warning 3dSkullStrip: Stubborn intersection remaining at smoothing of 120. Ignoring it.The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/step1/t2_masked.nii.gz -b /tmp/tmp.FqqBO1Mtvb/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.FqqBO1Mtvb/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/vote_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/voting/vote_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/step2/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/step2/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/step2/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/step2/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/t1_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/t1_skull.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/t1_t2/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./denoised/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./mrbias/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./stripped/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/t1_sri24/ants_0GenericAffine.mat ======================================================================== INFO: overlap between warped sri24 baseline mask and t1_brainmask: (dice = 0.967956) ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/t1_sri24/ants_0GenericAffine.dice ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/t1_sri24/ants_1Warp.nii.gz ======================================================================== ======================================================================== UPDATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/t1_sri24/ants_0GenericAffine.dice DUE TO LAB_S01450/standard/20161207_2762_12072016/structural/./registration/t1_sri24/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/t2_brain_exp_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/t2_affine_brain_exp_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/parc116.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/wm400.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/ventricles.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/suptent.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/parc_cortical.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/pbmap_CSF.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/pbmap_GM.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/pbmap_WM.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/inftent.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/suptent2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/postfossa_dmid.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/subject_t1/sri24/icv.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos/t1_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos/t1_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos/t1_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 2410 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 3 3 4 6 14 New number of Islands: 37 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos/t1_ven_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos/t1_gm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos/t1_wm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos/t1_seg_1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos_t2/t2_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos_t2/t2_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos_t2/t2_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 7535 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 4 4 4 5 6 6 7 8 11 14 22 New number of Islands: 88 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos_t2/t2_ven_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos_t2/t2_gm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/subject_t1/atropos_t2/t2_wm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/parc116.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/parc116.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/wm400.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/wm400.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/ventricles.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/ventricles.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/suptent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/suptent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/parc_cortical.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/parc_cortical.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/icv.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/icv.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/inftent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/inftent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/suptent2.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/suptent2.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/postfossa_dmid.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/subject_t1/sri24/atropos/postfossa_dmid.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/sri24_t1_padded.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/sri24_padded_to_t1/ants_rigid_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t2_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t2_brain_exp_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t2_affine_brain_exp_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t1_brain_t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/parc116.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/colic_thal.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/hipp_aplr_tmpl.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/wm400.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/ventricles.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/suptent.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/parc_cortical.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/pbmap_CSF.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/pbmap_GM.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/pbmap_WM.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/inftent.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/suptent2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/postfossa_dmid.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/icv.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos/t1_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos/t1_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos/t1_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 2328 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 3 4 6 12 New number of Islands: 38 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos/t1_ven_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos/t1_gm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos/t1_wm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_masked/t1_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_masked/t1_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_masked/t1_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 2283 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 3 4 5 9 New number of Islands: 38 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_masked/t1_ven_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_masked/t1_gm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_masked/t1_wm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_t2/t2_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_t2/t2_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_t2/t2_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 8197 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 4 4 4 5 5 6 7 7 9 11 13 19 New number of Islands: 114 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_t2/t2_ven_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_t2/t2_gm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_t2/t2_wm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/parc116.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/parc116.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/wm400.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/wm400.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/ventricles.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/ventricles.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/suptent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/suptent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/parc_cortical.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/parc_cortical.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/icv.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/icv.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/inftent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/inftent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/suptent2.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/suptent2.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/postfossa_dmid.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/postfossa_dmid.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/parc116_to_6rois.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos/parc116_to_32rois.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/parc116.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/parc116.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/wm400.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/wm400.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/ventricles.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/ventricles.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/suptent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/suptent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/parc_cortical.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/parc_cortical.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/icv.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/icv.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/inftent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/inftent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/suptent2.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/suptent2.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/postfossa_dmid.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/postfossa_dmid.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/parc116_to_6rois.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_t2/parc116_to_32rois.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/cere_bs_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t1_brain_cb_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t2_affine_brain_cb.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t1_brain_cb.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/suit_to_sri24_padded_cb/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./registration/suit_to_sri24_padded_cb/ants_1Warp.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/Cerebellum-SUIT.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/Cerebellum-SUIT_bin.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/SUIT_icbm_csf.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/SUIT_icbm_gm.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/SUIT_icbm_wm.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./reslice/sri24_padded/t1_brain_cb_mrbias_corrected.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_cb/t1_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_cb/t1_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20161207_2762_12072016/structural/./segment/sri24_padded/atropos_cb/t1_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 955 Islands in the image. 1 1 1 1 1 1 2 3 6 New number of Islands: 12 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_cb/Cerebellum-SUIT.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_cb/Cerebellum-SUIT.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_cb/Cerebellum-SUIT_bin.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/./volumetry/sri24_padded/atropos_cb/Cerebellum-SUIT_bin.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/freesurfer7/LAB_S01450_standard_20161207_2762_12072016/mri/orig/001.mgz ======================================================================== error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale mri_convert --delete-cmds -i LAB_S01450/standard/20161207_2762_12072016/structural/stripped/t1_brain.nii.gz -o LAB_S01450/standard/20161207_2762_12072016/structural/freesurfer7/LAB_S01450_standard_20161207_2762_12072016/mri/orig/001.mgz reading from LAB_S01450/standard/20161207_2762_12072016/structural/stripped/t1_brain.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to LAB_S01450/standard/20161207_2762_12072016/structural/freesurfer7/LAB_S01450_standard_20161207_2762_12072016/mri/orig/001.mgz... ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/freesurfer7/LAB_S01450_standard_20161207_2762_12072016/mri/brainmask.mgz ======================================================================== Running freesurfer stage 1 with pre-made brain mask... freesurfer: pushd LAB_S01450/standard/20161207_2762_12072016/structural/freesurfer7/LAB_S01450_standard_20161207_2762_12072016/mri; ln -s orig.mgz brainmask.auto.mgz; popd freesurfer: pushd LAB_S01450/standard/20161207_2762_12072016/structural/freesurfer7/LAB_S01450_standard_20161207_2762_12072016/mri; ln -s orig.mgz brainmask.mgz; popd Running freesurfer stage 1 with pre-made brain mask...done ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/freesurfer7/LAB_S01450_standard_20161207_2762_12072016/label/rh.entorhinal_exvivo.label ======================================================================== Running freesurfer stage 2 + 3... Running freesurfer stage 2 + 3...done ======================================================================== CREATE LAB_S01450/standard/20161207_2762_12072016/structural/segment/freesurfer7/aparc+aseg.nii.gz ======================================================================== error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale Number of labels: 0 Annot File: (null) Template Volume: LAB_S01450/standard/20161207_2762_12072016/structural/freesurfer7/LAB_S01450_standard_20161207_2762_12072016/mri/rawavg.mgz Outut Volume: LAB_S01450/standard/20161207_2762_12072016/structural/segment/freesurfer7/aparc+aseg.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /usr/local/tools/freesurfer/7.1.1/Ubuntu14/subjects 7.1.1 Template RAS-to-Vox: -------- -1.06667 -0.00000 -0.00000 128.00000; -0.00000 -0.00000 -1.06667 128.00000; -0.00000 0.83333 -0.00000 73.00001; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 1.05469 nHits Thresh: 0 Computing registration based on header RegMat: -------- 0.00000 1.00000 0.00000 0.00000; 1.00000 0.00000 0.00000 0.00002; 0.00000 0.00000 1.00000 0.00002; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- 0.00000 -1.06667 0.00000 128.00000; 0.00000 0.00000 -1.06667 127.99998; 0.83333 0.00000 0.00000 73.00002; 0.00000 0.00000 0.00000 1.00000; mri_label2vol done ======================================================================== TARGET LAB_S01450/standard/20161207_2762_12072016/structural/freesurfer7/LAB_S01450_standard_20161207_2762_12072016/measures/aseg.csv MISSING SOURCE /home/users/vmohanty/cases/case2/LAB_S00001/standard/20080609_3422_06092008/structural/freesurfer7/LAB_S00001_standard_20080609_3422_06092008/measures/aseg.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/denoised/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/step1/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/registration/t1_t2/affine.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/registration/t1_t2/warp.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/reslice/subject_t1/t2.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/denoised/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/step1/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/registration/t1_sri24_whole/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/registration/t1_sri24_whole/ants_1Warp.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/reslice/subject_t1/t1_sri24_whole/t1_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/reslice/subject_t1/t1_sri24_whole/t2_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/reslice/subject_t1/t1_sri24_whole/brainmask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/reslice/subject_t1/t1_sri24_whole/brainmask_10.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/denoised/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/step1/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/denoised/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/step1/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/robex_t1_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.7SrSKXCPSF ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 0 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 9 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 5 seconds Step 4 of 9: calculating features...Done! It took roughly 19 seconds Step 5 of 9: voxel classification...Done! It took roughly 11 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 2 seconds Step 7 of 9: free deformation...Done! It took roughly 0 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 0 seconds Output ready The whole process took roughly 48 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/robex_t1b_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.eEr7EnULnb ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 1 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 10 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 4 seconds Step 4 of 9: calculating features...Done! It took roughly 22 seconds Step 5 of 9: voxel classification...Done! It took roughly 12 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 1 seconds Step 7 of 9: free deformation...Done! It took roughly 0 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 0 seconds Output ready The whole process took roughly 52 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/bet_t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/bet_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/afni_t1_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/original/denoised/t1_masked.nii.gz -b /tmp/tmp.ImO1sQl6AJ/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.ImO1sQl6AJ/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/afni_t1b_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/step1/t1_masked.nii.gz -b /tmp/tmp.T03zMMC6DX/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.T03zMMC6DX/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/gcut_t1b_brain.nii.gz ======================================================================== error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale MRIchangeType: Building histogram 0 8181.21 1000, flo=0, fhi=0.999, dest_type=0 MRIchangeType: Building histogram 0 8181.21 1000, flo=0, fhi=0.999, dest_type=0 estimating WM mask white mean: 76.536692; seed number 382072 threshold set to: 76.536692*0.400000=30.614677 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale mri_convert --delete-cmds /tmp/tmp.6wzniRQ9uY/gcut_brain.mgz LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/gcut_t1b_brain.nii.gz reading from /tmp/tmp.6wzniRQ9uY/gcut_brain.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/gcut_t1b_brain.nii.gz... ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/gcut_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/bet_t2_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/bet_t2b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/afni_t2_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/original/denoised/t2_masked.nii.gz -b /tmp/tmp.mNSlY9G3lz/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.mNSlY9G3lz/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/afni_t2b_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/step1/t2_masked.nii.gz -b /tmp/tmp.b64nyJT4sS/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.b64nyJT4sS/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/vote_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/voting/vote_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/step2/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/step2/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/step2/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/step2/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/longitudinal/registration/baseline_to_t1/ants_0GenericAffine.mat ======================================================================== INFO: overlap between warped baseline mask and vote mask: (dice = 0.983921) ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/longitudinal/registration/baseline_to_t1/ants_0GenericAffine.dice ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/longitudinal/registration/baseline_to_t1/ants_1Warp.nii.gz ======================================================================== ======================================================================== UPDATE LAB_S01450/standard/20180829_5012_08292018/structural/original/longitudinal/registration/baseline_to_t1/ants_0GenericAffine.dice DUE TO LAB_S01450/standard/20180829_5012_08292018/structural/original/longitudinal/registration/baseline_to_t1/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/longitudinal/registration/baseline_to_t1/ants_1Warp.dice ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/t1_skull.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/registration/t1_t2/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/denoised/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/mrbias/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/original/stripped/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/intensity_corrected/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/registration/t1_t2/affine.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/registration/t1_t2/warp.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/reslice/subject_t1/t2.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/denoised/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/step1/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/registration/t1_sri24_whole/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/registration/t1_sri24_whole/ants_1Warp.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/reslice/subject_t1/t1_sri24_whole/t1_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/reslice/subject_t1/t1_sri24_whole/t2_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/reslice/subject_t1/t1_sri24_whole/brainmask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/reslice/subject_t1/t1_sri24_whole/brainmask_10.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/denoised/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/step1/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/denoised/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/step1/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/robex_t1_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.6zRYk8Dm8v ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 0 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 10 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 4 seconds Step 4 of 9: calculating features...Done! It took roughly 21 seconds Step 5 of 9: voxel classification...Done! It took roughly 11 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 4 seconds Step 7 of 9: free deformation...Done! It took roughly 1 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 0 seconds Output ready The whole process took roughly 53 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/robex_t1b_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.iPtULF5Ug4 ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 0 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 10 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 5 seconds Step 4 of 9: calculating features...Done! It took roughly 19 seconds Step 5 of 9: voxel classification...Done! It took roughly 12 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 1 seconds Step 7 of 9: free deformation...Done! It took roughly 0 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 3 seconds Step 9 of 9: warping back to original space...Done! It took roughly 0 seconds Output ready The whole process took roughly 50 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/bet_t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/bet_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/afni_t1_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/boosted/denoised/t1_masked.nii.gz -b /tmp/tmp.KUMe1MBqWB/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.KUMe1MBqWB/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/afni_t1b_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/step1/t1_masked.nii.gz -b /tmp/tmp.8M3Ry1JqYq/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.8M3Ry1JqYq/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/gcut_t1b_brain.nii.gz ======================================================================== error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale MRIchangeType: Building histogram 0 11188.3 1000, flo=0, fhi=0.999, dest_type=0 MRIchangeType: Building histogram 0 11188.3 1000, flo=0, fhi=0.999, dest_type=0 estimating WM mask white mean: 67.573927; seed number 428659 threshold set to: 67.573927*0.400000=27.029571 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale mri_convert --delete-cmds /tmp/tmp.iOHMYVN4AX/gcut_brain.mgz LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/gcut_t1b_brain.nii.gz reading from /tmp/tmp.iOHMYVN4AX/gcut_brain.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/gcut_t1b_brain.nii.gz... ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/gcut_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/bet_t2_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/bet_t2b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/afni_t2_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/boosted/denoised/t2_masked.nii.gz -b /tmp/tmp.j7T1DkZC2k/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.j7T1DkZC2k/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/afni_t2b_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/step1/t2_masked.nii.gz -b /tmp/tmp.a2x6iRNnt1/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.a2x6iRNnt1/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/vote_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/voting/vote_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/step2/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/step2/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/step2/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/step2/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/longitudinal/registration/baseline_to_t1/ants_0GenericAffine.mat ======================================================================== INFO: overlap between warped baseline mask and vote mask: (dice = 0.982925) ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/longitudinal/registration/baseline_to_t1/ants_0GenericAffine.dice ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/longitudinal/registration/baseline_to_t1/ants_1Warp.nii.gz ======================================================================== ======================================================================== UPDATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/longitudinal/registration/baseline_to_t1/ants_0GenericAffine.dice DUE TO LAB_S01450/standard/20180829_5012_08292018/structural/boosted/longitudinal/registration/baseline_to_t1/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/longitudinal/registration/baseline_to_t1/ants_1Warp.dice ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/t1_skull.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/registration/t1_t2/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/denoised/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/mrbias/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/boosted/stripped/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./denoised/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/step1/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./registration/t1_t2/affine.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./registration/t1_t2/warp.xform ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/t2.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./denoised/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/step1/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./registration/t1_sri24_whole/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./registration/t1_sri24_whole/ants_1Warp.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/t1_sri24_whole/t1_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/t1_sri24_whole/t2_whole.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/t1_sri24_whole/brainmask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/t1_sri24_whole/brainmask_10.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./denoised/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/step1/t1_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./denoised/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/step1/t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/robex_t1_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.of27EfEMep ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 0 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 10 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 4 seconds Step 4 of 9: calculating features...Done! It took roughly 19 seconds Step 5 of 9: voxel classification...Done! It took roughly 12 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 3 seconds Step 7 of 9: free deformation...Done! It took roughly 0 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 0 seconds Output ready The whole process took roughly 50 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/robex_t1b_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS /tmp/tmp.LJCayB8SMp ~/cases/case2 Step 1 of 9: reading in images...Done! It took roughly 1 seconds Step 2 of 9: registration... 2a) Similarity transform... 2b) Affine transform... 2c) Resampling volume... Registration done! It took roughly 10 seconds Step 3 of 9: rough bias field correction...Done! It took roughly 3 seconds Step 4 of 9: calculating features...Done! It took roughly 20 seconds Step 5 of 9: voxel classification...Done! It took roughly 12 seconds Step 6 of 9: fitting the shape model...Done! It took roughly 2 seconds Step 7 of 9: free deformation...Done! It took roughly 0 seconds Step 8 of 9: building volume from mesh...Done! It took roughly 2 seconds Step 9 of 9: warping back to original space...Done! It took roughly 0 seconds Output ready The whole process took roughly 50 seconds Freeing memory and deleting temporary files... ~/cases/case2 INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/bet_t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/bet_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/afni_t1_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/./denoised/t1_masked.nii.gz -b /tmp/tmp.8uQiBaurAG/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.8uQiBaurAG/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/afni_t1b_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/step1/t1_masked.nii.gz -b /tmp/tmp.gclW3i4MSt/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.gclW3i4MSt/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/gcut_t1b_brain.nii.gz ======================================================================== error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale MRIchangeType: Building histogram 0 11188.3 1000, flo=0, fhi=0.999, dest_type=0 MRIchangeType: Building histogram 0 11188.3 1000, flo=0, fhi=0.999, dest_type=0 estimating WM mask white mean: 68.558433; seed number 447450 threshold set to: 68.558433*0.400000=27.423373 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale mri_convert --delete-cmds /tmp/tmp.JD2ODrr1pt/gcut_brain.mgz LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/gcut_t1b_brain.nii.gz reading from /tmp/tmp.JD2ODrr1pt/gcut_brain.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/gcut_t1b_brain.nii.gz... ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/gcut_t1b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/bet_t2_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/bet_t2b_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/afni_t2_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/./denoised/t2_masked.nii.gz -b /tmp/tmp.jGoJTzwXSV/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.jGoJTzwXSV/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/afni_t2b_brain_mask.nii.gz ======================================================================== The output dataset is a mask reflecting where voxels in the input dataset lie in the brain. To obtain a masked version of the input with identical values inside the brain, you can either use 3dSkullStrip's -orig_vol option or run the following command: 3dcalc -a LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/step1/t2_masked.nii.gz -b /tmp/tmp.IlC8lVerd2/afni_brain_mask_tmp.nii.gz+orig -expr 'a*step(b)' \ -prefix /tmp/tmp.IlC8lVerd2/afni_brain_mask_tmp.nii.gz_orig_vol to generate a new masked version of the input. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/vote_brain_mask.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/voting/vote_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/step2/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/step2/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/step2/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/step2/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/baseline_to_t1/ants_0GenericAffine.mat ======================================================================== INFO: overlap between warped baseline mask and vote mask: (dice = 0.983278) ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/baseline_to_t1/ants_0GenericAffine.dice ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/baseline_to_t1/ants_1Warp.nii.gz ======================================================================== ======================================================================== UPDATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/baseline_to_t1/ants_0GenericAffine.dice DUE TO LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/baseline_to_t1/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/baseline_to_t1/ants_1Warp.dice ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/t1_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/t1_skull.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/t2_brain.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./registration/t1_t2/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./denoised/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./mrbias/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./stripped/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/corrected/t1_brain_reference.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/corrected/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/corrected/t2_brain_reference.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/corrected/t2_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/corrected/t2_affine_brain_reference.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/corrected/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/corrected/native/t1_brain_reference.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/corrected/native/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/t1_brain_to_baseline/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/t1_brain_to_baseline/ants_1Warp.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/t2_brain_exp_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/t2_affine_brain_exp_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/parc116.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/wm400.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/ventricles.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/suptent.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/parc_cortical.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/pbmap_CSF.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/pbmap_GM.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/pbmap_WM.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/inftent.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/suptent2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/postfossa_dmid.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/subject_t1/sri24/icv.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos/t1_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos/t1_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos/t1_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 2712 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 3 4 5 7 14 New number of Islands: 35 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos/t1_ven_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos/t1_gm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos/t1_wm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos/t1_seg_1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos_t2/t2_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos_t2/t2_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos_t2/t2_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 6305 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 4 4 5 5 6 7 8 11 16 New number of Islands: 103 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos_t2/t2_ven_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos_t2/t2_gm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/subject_t1/atropos_t2/t2_wm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/parc116.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/parc116.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/wm400.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/wm400.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/ventricles.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/ventricles.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/suptent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/suptent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/parc_cortical.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/parc_cortical.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/icv.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/icv.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/inftent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/inftent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/suptent2.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/suptent2.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/postfossa_dmid.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/subject_t1/sri24/atropos/postfossa_dmid.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/baseline_sri24_padded_to_t1/ants_rigid_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/t1_brain_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/t1.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/t2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/t2_affine.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/t2_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/corrected/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/corrected/t2_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/corrected/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/t2_brain_exp_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/t2_affine_brain_exp_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/corrected/t1_brain_t2_masked.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/parc116.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/colic_thal.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/hipp_aplr_tmpl.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/wm400.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/ventricles.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/suptent.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/parc_cortical.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/pbmap_CSF.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/pbmap_GM.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/pbmap_WM.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/inftent.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/suptent2.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/postfossa_dmid.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/icv.nii.gz ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos/t1_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos/t1_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos/t1_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 2566 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 3 3 4 5 9 New number of Islands: 36 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos/t1_ven_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos/t1_gm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos/t1_wm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_masked/t1_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_masked/t1_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_masked/t1_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 2009 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 3 4 6 13 New number of Islands: 31 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_masked/t1_ven_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_masked/t1_gm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_masked/t1_wm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_t2/t2_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_t2/t2_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_t2/t2_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 6720 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 4 4 5 5 6 7 9 12 18 New number of Islands: 109 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_t2/t2_ven_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_t2/t2_gm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_t2/t2_wm_parc.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/parc116.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/parc116.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/wm400.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/wm400.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/ventricles.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/ventricles.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/suptent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/suptent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/parc_cortical.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/parc_cortical.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/icv.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/icv.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/inftent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/inftent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/suptent2.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/suptent2.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/postfossa_dmid.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/postfossa_dmid.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/parc116_to_6rois.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos/parc116_to_32rois.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/parc116.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/parc116.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/wm400.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/wm400.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/ventricles.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/ventricles.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/suptent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/suptent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/parc_cortical.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/parc_cortical.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/icv.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/icv.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/inftent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/inftent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/suptent2.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/suptent2.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/postfossa_dmid.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/postfossa_dmid.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/parc116_to_6rois.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_t2/parc116_to_32rois.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_seg_clean_0000.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_seg_0000.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 2337 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 3 4 6 11 New number of Islands: 39 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_ven_parc_0000.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_gm_parc_0000.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_wm_parc_0000.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_seg_clean_0001.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_seg_0001.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 2331 Islands in the image. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 3 4 6 12 New number of Islands: 38 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_ven_parc_0001.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_gm_parc_0001.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos/t1_wm_parc_0001.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/parc116.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/parc116.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/wm400.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/wm400.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/ventricles.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/ventricles.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/suptent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/suptent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/parc_cortical.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/parc_cortical.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/icv.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/icv.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/inftent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/inftent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/suptent2.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/suptent2.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/postfossa_dmid.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20161207_2762_12072016/postfossa_dmid.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/parc116.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/parc116.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/wm400.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/wm400.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/ventricles.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/ventricles.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/suptent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/suptent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/parc_cortical.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/parc_cortical.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/icv.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/icv.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/inftent.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/inftent.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/suptent2.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/suptent2.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/postfossa_dmid.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos/20180829_5012_08292018/postfossa_dmid.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20161207_2762_12072016/20161207_2762_12072016/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20161207_2762_12072016/20180829_5012_08292018/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20161207_2762_12072016/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20180829_5012_08292018/20161207_2762_12072016/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20180829_5012_08292018/20180829_5012_08292018/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20180829_5012_08292018/t1_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20161207_2762_12072016/20161207_2762_12072016/t2_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20161207_2762_12072016/20180829_5012_08292018/t2_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20161207_2762_12072016/t2_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20180829_5012_08292018/20161207_2762_12072016/t2_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20180829_5012_08292018/20180829_5012_08292018/t2_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20180829_5012_08292018/t2_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20161207_2762_12072016/20161207_2762_12072016/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20161207_2762_12072016/20180829_5012_08292018/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20161207_2762_12072016/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20180829_5012_08292018/20161207_2762_12072016/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20180829_5012_08292018/20180829_5012_08292018/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/averaged/20180829_5012_08292018/t2_affine_brain.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/cere_bs_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/t1_brain_cb_mask.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/corrected/t2_affine_brain_cb.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/corrected/t1_brain_cb.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/sri24_padded_cb_to_baseline/ants_0GenericAffine.mat ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/registration/sri24_padded_cb_to_baseline/ants_1Warp.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/Cerebellum-SUIT.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/Cerebellum-SUIT_bin.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/SUIT_icbm_csf.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/SUIT_icbm_gm.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/SUIT_icbm_wm.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./reslice/sri24_padded/corrected/t1_brain_cb_mrbias_corrected.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_cb/t1_seg.nii.gz ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_cb/t1_seg_clean.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20180829_5012_08292018/structural/./segment/sri24_padded/atropos_cb/t1_seg.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 960 Islands in the image. 1 1 1 1 1 1 2 3 6 New number of Islands: 9 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_cb/Cerebellum-SUIT.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_cb/Cerebellum-SUIT.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_cb/Cerebellum-SUIT_bin.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./volumetry/sri24_padded/atropos_cb/Cerebellum-SUIT_bin.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos_cb/t1_seg.nii.gz ======================================================================== Exception caught of type 16ConvertException Exception detail: Unable to read image LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos_cb/t1_seg_clean_0000.nii.gz; IO factory can not create IO object. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos_cb/t1_seg_clean_0000.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos_cb/t1_seg_0000.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 817 Islands in the image. 1 1 1 1 1 2 3 10 New number of Islands: 9 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved Exception caught of type 16ConvertException Exception detail: Unable to read image LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos_cb/t1_seg_clean_0001.nii.gz; IO factory can not create IO object. ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos_cb/t1_seg_clean_0001.nii.gz ======================================================================== Done reading the file LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/segment/sri24_padded/atropos_cb/t1_seg_0001.nii.gz ====================================================== vtkImageIslandFilter::ExecuteData: Delete Islands smaller 25 in Mode 3D There are currently 880 Islands in the image. 1 1 1 1 1 2 2 4 New number of Islands: 9 vtkImageIslandFilter::ExecuteData: Finished Deleting ====================================================== Warning : Header information is not preserved ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos_cb/20161207_2762_12072016/Cerebellum-SUIT.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos_cb/20161207_2762_12072016/Cerebellum-SUIT.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos_cb/20161207_2762_12072016/Cerebellum-SUIT_bin.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos_cb/20161207_2762_12072016/Cerebellum-SUIT_bin.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos_cb/20180829_5012_08292018/Cerebellum-SUIT.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos_cb/20180829_5012_08292018/Cerebellum-SUIT.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos_cb/20180829_5012_08292018/Cerebellum-SUIT_bin.tab ======================================================================== INFO: number of threads set to 8 according to environment variable CMTK_NUM_THREADS ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/./longitudinal/volumetry/sri24_padded/atropos_cb/20180829_5012_08292018/Cerebellum-SUIT_bin.csv ======================================================================== ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/freesurfer7/LAB_S01450_standard_20180829_5012_08292018/mri/orig/001.mgz ======================================================================== error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale error: No such file or directory error: Could not set locale mri_convert --delete-cmds -i LAB_S01450/standard/20180829_5012_08292018/structural/longitudinal/corrected/t1_brain.nii.gz -o LAB_S01450/standard/20180829_5012_08292018/structural/freesurfer7/LAB_S01450_standard_20180829_5012_08292018/mri/orig/001.mgz reading from LAB_S01450/standard/20180829_5012_08292018/structural/longitudinal/corrected/t1_brain.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to LAB_S01450/standard/20180829_5012_08292018/structural/freesurfer7/LAB_S01450_standard_20180829_5012_08292018/mri/orig/001.mgz... ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/freesurfer7/LAB_S01450_standard_20180829_5012_08292018/mri/brainmask.mgz ======================================================================== Running freesurfer stage 1 with pre-made brain mask... freesurfer: pushd LAB_S01450/standard/20180829_5012_08292018/structural/freesurfer7/LAB_S01450_standard_20180829_5012_08292018/mri; ln -s orig.mgz brainmask.auto.mgz; popd freesurfer: pushd LAB_S01450/standard/20180829_5012_08292018/structural/freesurfer7/LAB_S01450_standard_20180829_5012_08292018/mri; ln -s orig.mgz brainmask.mgz; popd Running freesurfer stage 1 with pre-made brain mask...done ======================================================================== CREATE LAB_S01450/standard/20180829_5012_08292018/structural/freesurfer7/LAB_S01450_standard_20180829_5012_08292018/label/rh.entorhinal_exvivo.label ======================================================================== Running freesurfer stage 2 + 3...