Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

Hippocampal subfields error
by Emily K Clarke 09 Sep '20

09 Sep '20

External Email - Use Caution Hi Eugenio, We’re still running into the issue where running recon-all with the hippocampal subfields tag isn’t actually generating any of the hippocampal files. I’ve included our full recon-all log below. We already examined the scans, and they look perfectly normal – do you know why this might be happening? Thanks, Emily Clarke-Rubright Morey Neuroimaging Lab The whole log message: #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Mon Aug 10 18:54:21 EDT 2020 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/packages/freesurfer_v6.0.0/MCRv80/runtime/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/bin/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/os/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib64/qt5/plugins/platforms:/usr/local/packages/ants-2.3.4/lib:/usr/lib64/openmpi/lib: Warning: application is running on a locale different from the original platform locale. Warning: No display specified. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG This file does not contain MRI parameters $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ --mov: Using imageDump.mgz as movable/source volume. --dst: Using /mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… as target volume. --lta: Output transform as trash.lta . --mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz ! --sat: Using saturation 50 in M-estimator! reading source 'imageDump.mgz'... reading target '/mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/…'. .. Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE ) Type Source : 0 Type Target : 3 ensure both FLOAT (3) Reordering axes in mov to better fit dst... ( -1 3 -2 ) MRIreorder() ----------- xdim=-1 ydim=3 zdim=-2 src 131 241 99, 0.250000 0.250000 0.250000 dst 131 99 241, 0.250000 0.250000 0.250000 Determinant after swap : 0.015625 Mov: (0.25, 0.25, 0.25)mm and dim (131, 99, 241) Dst: (1, 1, 1)mm and dim (38, 40, 59) Asserting both images: 1mm isotropic - reslicing Mov ... -- changing data type from 0 to 3 (noscale = 0)... -- Original : (0.25, 0.25, 0.25)mm and (131, 99, 241) voxels. -- Resampled: (1, 1, 1)mm and (38, 40, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - reslicing Dst ... -- Original : (1, 1, 1)mm and (38, 40, 59) voxels. -- Resampled: (1, 1, 1)mm and (38, 40, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 1 ) - initial transform: Ti = [ ... 1.0000000000000 0 0 1.1459029727155 0 1.0000000000000 0 -0.0876360601093 0 0 1.0000000000000 -2.9034875996918 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 1 S( 19 20 30 ) T( 19 20 30 ) Iteration(f): 1 -- diff. to prev. transform: 7.11234 Iteration(f): 2 -- diff. to prev. transform: 5.92976 Iteration(f): 3 -- diff. to prev. transform: 7.00993 Iteration(f): 4 -- diff. to prev. transform: 4.91305 Iteration(f): 5 -- diff. to prev. transform: 0.781018 max it: 5 reached! Resolution: 0 S( 38 40 61 ) T( 38 40 61 ) Iteration(f): 1 -- diff. to prev. transform: 8.1296 Iteration(f): 2 -- diff. to prev. transform: 1.32542 Iteration(f): 3 -- diff. to prev. transform: 0.660013 Iteration(f): 4 -- diff. to prev. transform: 0.272219 Iteration(f): 5 -- diff. to prev. transform: 0.0943126 max it: 5 reached! - final transform: Tf = [ ... 0.9986737402682 -0.0371977207162 0.0355962086772 0.4749903609000 0.0194355513105 0.9126027300469 0.4083852549446 -14.0571487737101 -0.0476761978762 -0.4071517980857 0.9121153400046 9.9144950322154 0 0 0 1.0000000000000 ] - final iscale: If = 1 ********************************************************** * * WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! * ********************************************************** Final Transform: Adjusting final transform due to initial resampling (voxel or size changes) ... M = [ ... -0.2496684350671 0.0088990521693 0.0092994301791 34.3717771918614 -0.0048588878276 0.1020963137361 -0.2281506825117 16.0960341057205 0.0119190494690 0.2280288350011 0.1017879495214 -5.4978401025085 0 0 0 1.0000000000000 ] Determinant : -0.015625 writing output transformation to trash.lta ... converting VOX to RAS and saving RAS2RAS... mapmovhdr: Changing vox2ras MOV header (to map to DST) ... To check aligned result, run: freeview -v /mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… imageDump_coregistered.mgz Registration took 0 minutes and 1 seconds. Thank you for using RobustRegister! If you find it useful and use it for a publication, please cite: Highly Accurate Inverse Consistent Registration: A Robust Approach M. Reuter, H.D. Rosas, B. Fischl. NeuroImage 53(4):1181-1196, 2010. http://dx.doi.org/10.1016/j.neuroimage.2010.07.020 http://reuter.mit.edu/papers/reuter-robreg10.pdf $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ --mov: Using imageDump.mgz as movable/source volume. --dst: Using /mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… as target volume. --lta: Output transform as trash.lta . --mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz ! --affine: Enableing affine transform! --sat: Using saturation 50 in M-estimator! reading source 'imageDump.mgz'... reading target '/mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/…'. .. Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE ) Type Source : 0 Type Target : 3 ensure both FLOAT (3) Reordering axes in mov to better fit dst... ( -1 3 -2 ) MRIreorder() ----------- xdim=-1 ydim=3 zdim=-2 src 131 241 99, 0.250000 0.250000 0.250000 dst 131 99 241, 0.250000 0.250000 0.250000 Determinant after swap : 0.015625 Mov: (0.25, 0.25, 0.25)mm and dim (131, 99, 241) Dst: (1, 1, 1)mm and dim (38, 40, 59) Asserting both images: 1mm isotropic - reslicing Mov ... -- changing data type from 0 to 3 (noscale = 0)... -- Original : (0.25, 0.25, 0.25)mm and (131, 99, 241) voxels. -- Resampled: (1, 1, 1)mm and (38, 40, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - reslicing Dst ... -- Original : (1, 1, 1)mm and (38, 40, 59) voxels. -- Resampled: (1, 1, 1)mm and (38, 40, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 1 ) - initial transform: Ti = [ ... 1.0000000000000 0 0 1.1459028059189 0 1.0000000000000 0 -0.0876339827813 0 0 1.0000000000000 -2.9034861096682 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 1 S( 19 20 30 ) T( 19 20 30 ) Iteration(f): 1 -- diff. to prev. transform: 7.39891 Iteration(f): 2 -- diff. to prev. transform: 6.07128 Iteration(f): 3 -- diff. to prev. transform: 6.45354 Iteration(f): 4 -- diff. to prev. transform: 9.61165 Iteration(f): 5 -- diff. to prev. transform: 6.45157 max it: 5 reached! Resolution: 0 S( 38 40 61 ) T( 38 40 61 ) Iteration(f): 1 -- diff. to prev. transform: 18.1397 Iteration(f): 2 -- diff. to prev. transform: 10.4781 Iteration(f): 3 -- diff. to prev. transform: 4.71708 Iteration(f): 4 -- diff. to prev. transform: 2.16703 Iteration(f): 5 -- diff. to prev. transform: 0.732237 max it: 5 reached! - final transform: Tf = [ ... 1.1003251237945 0.4596695415609 0.1319823678432 -15.3375075204562 -0.0809129505733 1.0958357713115 0.4294815397408 -16.7169936140805 -0.0871431123400 -0.3796938017010 0.9044729973197 10.3182069614882 0 0 0 1.0000000000000 ] - final iscale: If = 1 ********************************************************** * * WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! * ********************************************************** Final Transform: Adjusting final transform due to initial resampling (voxel or size changes) ... M = [ ... -0.2750812479116 0.0329955927294 -0.1149173912565 38.1277797083535 0.0202282358422 0.1073703848787 -0.2739589559572 15.8057165631404 0.0217857755217 0.2261182492690 0.0949234628220 -5.6011779490725 0 0 0 1.0000000000000 ] Determinant : -0.0203612 Decompose into Rot * Shear * Scale : Rot = [ ... -0.9711353975406 0.1063152910440 -0.2135254048909 0.2376286779964 0.3535137619413 -0.9047434064484 0.0207038894236 0.9293681073764 0.3685732898005 ] Shear = [ ... 1.0000000000000 -0.0073421724799 0.1576683162397 -0.0067818833526 1.0000000000000 -0.0678198022274 0.1779196232492 -0.0828533754661 1.0000000000000 ] Scale = diag([ 0.2723989962754 0.2516119340902 0.3073865945084 ]) writing output transformation to trash.lta ... converting VOX to RAS and saving RAS2RAS... mapmovhdr: Changing vox2ras MOV header (to map to DST) ... To check aligned result, run: freeview -v /mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… imageDump_coregistered.mgz Registration took 0 minutes and 1 seconds. Thank you for using RobustRegister! If you find it useful and use it for a publication, please cite: Highly Accurate Inverse Consistent Registration: A Robust Approach M. Reuter, H.D. Rosas, B. Fischl. NeuroImage 53(4):1181-1196, 2010. http://dx.doi.org/10.1016/j.neuroimage.2010.07.020 http://reuter.mit.edu/papers/reuter-robreg10.pdf Reading contexts of file /usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt Constructing image-to-world transform from header information (asegMod.mgz) Returning the following transform: AffineTransform (0x2b5e6a48e220) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 422 Debug: Off Object Name: Observers: none Matrix: -1 -1.86265e-09 1.3024e-09 -3.49428e-09 -1.16415e-10 1 1.86265e-09 -1 -1.16415e-10 Offset: [132.04, -111.801, 144.75] Center: [0, 0, 0] Translation: [132.04, -111.801, 144.75] Inverse: -1 1.3024e-09 1.86265e-09 -1.86265e-09 -1.16415e-10 -1 -3.49428e-09 1 -1.16415e-10 Singular: 0 Constructing image-to-world transform from header information (/mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… ) Returning the following transform: AffineTransform (0x2b5e6a48e220) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 579 Debug: Off Object Name: Observers: none Matrix: 0.275081 -0.0329956 0.114917 0.0217858 0.226118 0.0949235 -0.0202282 -0.10737 0.273959 Offset: [-38.0874, -33.402, 1.94475] Center: [0, 0, 0] Translation: [-38.0874, -33.402, 1.94475] Inverse: 3.54297 -0.162038 -1.43002 -0.38743 3.81537 -1.15946 0.109759 1.48336 3.09018 Singular: 0 Transform before cropping: AffineTransform (0x2b5e6a48e220) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 581 Debug: Off Object Name: Observers: none Matrix: -0.275081 0.0329956 -0.114917 0.0202282 0.10737 -0.273959 0.0217858 0.226118 0.0949235 Offset: [170.128, 142.806, 78.3988] Center: [0, 0, 0] Translation: [170.128, 142.806, 78.3988] Inverse: -3.54297 1.43002 -0.162038 0.38743 1.15946 3.81537 -0.109759 -3.09018 1.48336 Singular: 0 WorldToImageTransform before cropping: AffineTransform (0x2b5e6a47e8f0) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 583 Debug: Off Object Name: Observers: none Matrix: -1 1.3024e-09 1.86265e-09 -1.86265e-09 -1.16415e-10 -1 -3.49428e-09 1 -1.16415e-10 Offset: [132.04, 144.75, 111.801] Center: [0, 0, 0] Translation: [132.04, 144.75, 111.801] Inverse: -1 -1.86265e-09 1.3024e-09 -3.49428e-09 -1.16415e-10 1 1.86265e-09 -1 -1.16415e-10 Singular: 0 m_BoundingBoxSize: [131, 241,99] minimalMappedCoordinate: [123.105, 115.958,78.3988] maximalMappedCoordinate: [178.047, 171.204,144.802] Cropping with min [118 110 72] and max [184 177 151] m_OriginalImageRegion before checking margins: ImageRegion (0x2b5e69a829b8) Dimension: 3 Index: [118, 110, 72] Size: [67, 68, 80] m_CroppedImageRegion before checking margins: ImageRegion (0x2b5e69a82980) Dimension: 3 Index: [0, 0, 0] Size: [67, 68, 80] m_OriginalImageRegion after checking margins: ImageRegion (0x2b5e69a829b8) Dimension: 3 Index: [118, 110, 72] Size: [67, 68, 80] m_CroppedImageRegion after checking margins: ImageRegion (0x2b5e69a82980) Dimension: 3 Index: [0, 0, 0] Size: [67, 68, 80] Transform after cropping: AffineTransform (0x2b5e6a48e220) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 740 Debug: Off Object Name: Observers: none Matrix: -0.275081 0.0329956 -0.114917 0.0202282 0.10737 -0.273959 0.0217858 0.226118 0.0949235 Offset: [52.1278, 32.8057, 6.39882] Center: [0, 0, 0] Translation: [52.1278, 32.8057, 6.39882] Inverse: -3.54297 1.43002 -0.162038 0.38743 1.15946 3.81537 -0.109759 -3.09018 1.48336 Singular: 0 WorldToImageTransform after cropping: AffineTransform (0x2b5e6a47e8f0) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 741 Debug: Off Object Name: Observers: none Matrix: -1 1.3024e-09 1.86265e-09 -1.86265e-09 -1.16415e-10 -1 -3.49428e-09 1 -1.16415e-10 Offset: [14.0404, 34.7505, 39.8009] Center: [0, 0, 0] Translation: [14.0404, 34.7505, 39.8009] Inverse: -1 -1.86265e-09 1.3024e-09 -3.49428e-09 -1.16415e-10 1 1.86265e-09 -1 -1.16415e-10 Singular: 0 Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Careful here: the applied transformation will turn positive tetrahedra into negative ones. -0.275081 0.0329956 -0.114917 0.0202282 0.10737 -0.273959 0.0217858 0.226118 0.0949235 determinant: -0.0203612 Starting to swap the point assignments of each tetrahedron... Warning: This concatenation operation includes an empty array with an incorrect number of rows. Concatenation including empty arrays will require all arrays to have the same number of rows in a future release. [ > In segmentSubjectT1_autoEstimateAlveusML at 325] Reading contexts of file /usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt -------------- Making Lateral-nucleus map to reduced label 1 Making Paralaminar-nucleus map to reduced label 1 Making Basal-nucleus map to reduced label 1 Making Accessory-Basal-nucleus map to reduced label 1 Making Corticoamygdaloid-transitio map to reduced label 1 Making Central-nucleus map to reduced label 1 Making Cortical-nucleus map to reduced label 1 Making Medial-nucleus map to reduced label 1 Making Anterior-amygdaloid-area-AAA map to reduced label 1 -------------- Making alveus map to reduced label 2 Making Hippocampal_tail map to reduced label 2 Making HATA map to reduced label 2 Making fimbria map to reduced label 2 Making parasubiculum map to reduced label 2 Making hippocampal-fissure map to reduced label 2 -------------- Making Left-Cerebral-Cortex map to reduced label 3 -------------- Making Left-Cerebral-White-Matter map to reduced label 4 -------------- Making Left-Lateral-Ventricle map to reduced label 5 -------------- Making Left-choroid-plexus map to reduced label 6 -------------- Making Unknown map to reduced label 7 -------------- Making Left-VentralDC map to reduced label 8 -------------- Making Left-Putamen map to reduced label 9 -------------- Making Left-Pallidum map to reduced label 10 -------------- Making Left-Thalamus-Proper map to reduced label 11 -------------- Making Left-Accumbens-area map to reduced label 12 -------------- Making Left-Caudate map to reduced label 13 Error using segmentSubjectT1_autoEstimateAlveusML (line 348) The vector of prior probabilities in the mesh nodes must always sum to one over all classes #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Mon Aug 10 18:54:37 EDT 2020 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/packages/freesurfer_v6.0.0/MCRv80/runtime/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/bin/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/os/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib64/qt5/plugins/platforms:/usr/local/packages/ants-2.3.4/lib:/usr/lib64/openmpi/lib: Warning: application is running on a locale different from the original platform locale. Warning: No display specified. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG This file does not contain MRI parameters $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ --mov: Using imageDump.mgz as movable/source volume. --dst: Using /mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… as target volume. --lta: Output transform as trash.lta . --mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz ! --sat: Using saturation 50 in M-estimator! reading source 'imageDump.mgz'... reading target '/mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/…'. .. Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE ) Type Source : 4 Type Target : 3 ensure both FLOAT (3) Reordering axes in mov to better fit dst... ( 1 3 -2 ) MRIreorder() ----------- xdim=1 ydim=3 zdim=-2 src 131 241 99, 0.250000 0.250000 0.250000 dst 131 99 241, 0.250000 0.250000 0.250000 Determinant after swap : 0.015625 Mov: (0.25, 0.25, 0.25)mm and dim (131, 99, 241) Dst: (1, 1, 1)mm and dim (38, 43, 57) Asserting both images: 1mm isotropic - reslicing Mov ... -- changing data type from 4 to 3 (noscale = 0)... -- Original : (0.25, 0.25, 0.25)mm and (131, 99, 241) voxels. -- Resampled: (1, 1, 1)mm and (38, 43, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - reslicing Dst ... -- Original : (1, 1, 1)mm and (38, 43, 57) voxels. -- Resampled: (1, 1, 1)mm and (38, 43, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 1 ) - initial transform: Ti = [ ... 1.0000000000000 0 0 0.1781192630761 0 1.0000000000000 0 1.0539982530706 0 0 1.0000000000000 -3.1974090629449 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 1 S( 19 21 30 ) T( 19 21 30 ) Iteration(f): 1 -- diff. to prev. transform: 13.2959 Iteration(f): 2 -- diff. to prev. transform: 9.20966 Iteration(f): 3 -- diff. to prev. transform: 6.22883 Iteration(f): 4 -- diff. to prev. transform: 8.12577 Iteration(f): 5 -- diff. to prev. transform: 6.11784 max it: 5 reached! Resolution: 0 S( 38 43 61 ) T( 38 43 61 ) Iteration(f): 1 -- diff. to prev. transform: 5.83495 Iteration(f): 2 -- diff. to prev. transform: 1.34307 Iteration(f): 3 -- diff. to prev. transform: 0.589867 Iteration(f): 4 -- diff. to prev. transform: 0.289573 Iteration(f): 5 -- diff. to prev. transform: 0.137676 max it: 5 reached! - final transform: Tf = [ ... 0.9980802661280 -0.0059694736544 0.0616453384301 -1.7131111872539 -0.0239991870640 0.8803011391816 0.4738079182283 -13.5066607583463 -0.0570948455303 -0.4743777711274 0.8784679327523 13.0909553444701 0 0 0 1.0000000000000 ] - final iscale: If = 1 ********************************************************** * * WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! * ********************************************************** Final Transform: Adjusting final transform due to initial resampling (voxel or size changes) ... M = [ ... 0.2495200665320 0.0154113346075 0.0014923684136 0.7292410424572 -0.0059997967660 0.1184519795571 -0.2200752847954 16.2081470043947 -0.0142737113826 0.2196169831881 0.1185944427819 -4.6804480513511 0 0 0 1.0000000000000 ] Determinant : 0.015625 writing output transformation to trash.lta ... converting VOX to RAS and saving RAS2RAS... mapmovhdr: Changing vox2ras MOV header (to map to DST) ... To check aligned result, run: freeview -v /mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… imageDump_coregistered.mgz Registration took 0 minutes and 1 seconds. Thank you for using RobustRegister! If you find it useful and use it for a publication, please cite: Highly Accurate Inverse Consistent Registration: A Robust Approach M. Reuter, H.D. Rosas, B. Fischl. NeuroImage 53(4):1181-1196, 2010. http://dx.doi.org/10.1016/j.neuroimage.2010.07.020 http://reuter.mit.edu/papers/reuter-robreg10.pdf $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ --mov: Using imageDump.mgz as movable/source volume. --dst: Using /mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… as target volume. --lta: Output transform as trash.lta . --mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz ! --affine: Enableing affine transform! --sat: Using saturation 50 in M-estimator! reading source 'imageDump.mgz'... reading target '/mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/…'. .. Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE ) Type Source : 4 Type Target : 3 ensure both FLOAT (3) Reordering axes in mov to better fit dst... ( 1 3 -2 ) MRIreorder() ----------- xdim=1 ydim=3 zdim=-2 src 131 241 99, 0.250000 0.250000 0.250000 dst 131 99 241, 0.250000 0.250000 0.250000 Determinant after swap : 0.015625 Mov: (0.25, 0.25, 0.25)mm and dim (131, 99, 241) Dst: (1, 1, 1)mm and dim (38, 43, 57) Asserting both images: 1mm isotropic - reslicing Mov ... -- changing data type from 4 to 3 (noscale = 0)... -- Original : (0.25, 0.25, 0.25)mm and (131, 99, 241) voxels. -- Resampled: (1, 1, 1)mm and (38, 43, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - reslicing Dst ... -- Original : (1, 1, 1)mm and (38, 43, 57) voxels. -- Resampled: (1, 1, 1)mm and (38, 43, 61) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 1 ) - initial transform: Ti = [ ... 1.0000000000000 0 0 0.1781175809123 0 1.0000000000000 0 1.0539986543476 0 0 1.0000000000000 -3.1974083471847 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 1 S( 19 21 30 ) T( 19 21 30 ) Iteration(f): 1 -- diff. to prev. transform: 9.84742 Iteration(f): 2 -- diff. to prev. transform: 7.72517 Iteration(f): 3 -- diff. to prev. transform: 8.94618 Iteration(f): 4 -- diff. to prev. transform: 7.30294 Iteration(f): 5 -- diff. to prev. transform: 5.69484 max it: 5 reached! Resolution: 0 S( 38 43 61 ) T( 38 43 61 ) Iteration(f): 1 -- diff. to prev. transform: 11.7013 Iteration(f): 2 -- diff. to prev. transform: 3.26787 Iteration(f): 3 -- diff. to prev. transform: 1.06278 Iteration(f): 4 -- diff. to prev. transform: 0.347277 Iteration(f): 5 -- diff. to prev. transform: 0.0826464 max it: 5 reached! - final transform: Tf = [ ... 1.1636664104160 -0.3014738824441 0.0004403516595 4.0520187720971 -0.0480158583329 1.0596278475093 0.4954259490783 -17.9010148715481 -0.2453688431946 -0.4779665918288 0.8802303084621 16.7816318160186 0 0 0 1.0000000000000 ] - final iscale: If = 1 ********************************************************** * * WARNING: Registration did not converge in 5 steps! * Problem might be ill posed. * Please inspect output manually! * ********************************************************** Final Transform: Adjusting final transform due to initial resampling (voxel or size changes) ... M = [ ... 0.2909164812245 0.0001100842157 0.0753684565922 -3.0302464159984 -0.0120039592287 0.1238564808785 -0.2649069144859 17.7887142169889 -0.0613421845898 0.2200575304725 0.1194916267047 -1.6040021052477 0 0 0 1.0000000000000 ] Determinant : 0.0216399 Decompose into Rot * Shear * Scale : Rot = [ ... 0.9808313831675 0.1119800663090 0.1594686882846 0.0897438323260 0.4668219029177 -0.8797859714247 -0.1729619679387 0.8772330224665 0.4478240524369 ] Shear = [ ... 1.0000000000000 -0.1069794540990 0.0987385001868 -0.0910164402411 1.0000000000000 -0.0348388469911 0.0999837864599 -0.0414655431721 1.0000000000000 ] Scale = diag([ 0.2948725983257 0.2508729779031 0.2985915205121 ]) writing output transformation to trash.lta ... converting VOX to RAS and saving RAS2RAS... mapmovhdr: Changing vox2ras MOV header (to map to DST) ... To check aligned result, run: freeview -v /mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… imageDump_coregistered.mgz Registration took 0 minutes and 1 seconds. Thank you for using RobustRegister! If you find it useful and use it for a publication, please cite: Highly Accurate Inverse Consistent Registration: A Robust Approach M. Reuter, H.D. Rosas, B. Fischl. NeuroImage 53(4):1181-1196, 2010. http://dx.doi.org/10.1016/j.neuroimage.2010.07.020 http://reuter.mit.edu/papers/reuter-robreg10.pdf Reading contexts of file /usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt Constructing image-to-world transform from header information (asegMod.mgz) Returning the following transform: AffineTransform (0x2b82ee48f820) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 422 Debug: Off Object Name: Observers: none Matrix: -1 -1.86265e-09 1.3024e-09 -3.49428e-09 -1.16415e-10 1 1.86265e-09 -1 -1.16415e-10 Offset: [132.04, -111.801, 144.75] Center: [0, 0, 0] Translation: [132.04, -111.801, 144.75] Inverse: -1 1.3024e-09 1.86265e-09 -1.86265e-09 -1.16415e-10 -1 -3.49428e-09 1 -1.16415e-10 Singular: 0 Constructing image-to-world transform from header information (/mnt/BIAC/.users/ch186/ duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/… ) Returning the following transform: AffineTransform (0x2b82ee48f820) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 579 Debug: Off Object Name: Observers: none Matrix: -0.290916 -0.000110086 -0.0753684 -0.0613422 0.220058 0.119492 0.012004 -0.123856 0.264907 Offset: [49.0706, -22.4049, 0.96176] Center: [0, 0, 0] Translation: [49.0706, -22.4049, 0.96176] Inverse: -3.37777 -0.432721 -0.765819 -0.81721 3.51948 -1.82003 -0.229025 1.66513 2.95866 Singular: 0 Transform before cropping: AffineTransform (0x2b82ee48f820) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 581 Debug: Off Object Name: Observers: none Matrix: 0.290916 0.000110086 0.0753685 -0.012004 0.123856 -0.264907 -0.0613422 0.220058 0.119492 Offset: [82.9698, 143.789, 89.396] Center: [0, 0, 0] Translation: [82.9698, 143.789, 89.396] Inverse: 3.37777 0.765819 -0.432721 0.81721 1.82003 3.51948 0.229025 -2.95866 1.66513 Singular: 0 WorldToImageTransform before cropping: AffineTransform (0x2b82ec807bf0) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 583 Debug: Off Object Name: Observers: none Matrix: -1 1.3024e-09 1.86265e-09 -1.86265e-09 -1.16415e-10 -1 -3.49428e-09 1 -1.16415e-10 Offset: [132.04, 144.75, 111.801] Center: [0, 0, 0] Translation: [132.04, 144.75, 111.801] Inverse: -1 -1.86265e-09 1.3024e-09 -3.49428e-09 -1.16415e-10 1 1.86265e-09 -1 -1.16415e-10 Singular: 0 m_BoundingBoxSize: [131, 241,99] minimalMappedCoordinate: [82.9698, 116.267,81.4215] maximalMappedCoordinate: [128.201, 173.514,153.92] Cropping with min [78 111 74] and max [133 179 161] m_OriginalImageRegion before checking margins: ImageRegion (0x2b82ec809218) Dimension: 3 Index: [78, 111, 74] Size: [56, 69, 88] m_CroppedImageRegion before checking margins: ImageRegion (0x2b82ec8091e0) Dimension: 3 Index: [0, 0, 0] Size: [56, 69, 88] m_OriginalImageRegion after checking margins: ImageRegion (0x2b82ec809218) Dimension: 3 Index: [78, 111, 74] Size: [56, 69, 88] m_CroppedImageRegion after checking margins: ImageRegion (0x2b82ec8091e0) Dimension: 3 Index: [0, 0, 0] Size: [56, 69, 88] Transform after cropping: AffineTransform (0x2b82ee48f820) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 740 Debug: Off Object Name: Observers: none Matrix: 0.290916 0.000110086 0.0753685 -0.012004 0.123856 -0.264907 -0.0613422 0.220058 0.119492 Offset: [4.96976, 32.7887, 15.396] Center: [0, 0, 0] Translation: [4.96976, 32.7887, 15.396] Inverse: 3.37777 0.765819 -0.432721 0.81721 1.82003 3.51948 0.229025 -2.95866 1.66513 Singular: 0 WorldToImageTransform after cropping: AffineTransform (0x2b82ec807bf0) RTTI typeinfo: itk::AffineTransform<double, 3u> Reference Count: 1 Modified Time: 741 Debug: Off Object Name: Observers: none Matrix: -1 1.3024e-09 1.86265e-09 -1.86265e-09 -1.16415e-10 -1 -3.49428e-09 1 -1.16415e-10 Offset: [54.0404, 33.7505, 37.8009] Center: [0, 0, 0] Translation: [54.0404, 33.7505, 37.8009] Inverse: -1 -1.86265e-09 1.3024e-09 -3.49428e-09 -1.16415e-10 1 1.86265e-09 -1 -1.16415e-10 Singular: 0 Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Transforming points Warning: This concatenation operation includes an empty array with an incorrect number of rows. Concatenation including empty arrays will require all arrays to have the same number of rows in a future release. [ > In segmentSubjectT1_autoEstimateAlveusML at 325] Reading contexts of file /usr/local/packages/freesurfer_v6.0.0/average/HippoSF/atlas/compressionLookupTable.txt -------------- Making Lateral-nucleus map to reduced label 1 Making Paralaminar-nucleus map to reduced label 1 Making Basal-nucleus map to reduced label 1 Making Accessory-Basal-nucleus map to reduced label 1 Making Corticoamygdaloid-transitio map to reduced label 1 Making Central-nucleus map to reduced label 1 Making Cortical-nucleus map to reduced label 1 Making Medial-nucleus map to reduced label 1 Making Anterior-amygdaloid-area-AAA map to reduced label 1 -------------- Making alveus map to reduced label 2 Making Hippocampal_tail map to reduced label 2 Making HATA map to reduced label 2 Making fimbria map to reduced label 2 Making parasubiculum map to reduced label 2 Making hippocampal-fissure map to reduced label 2 -------------- Making Left-Cerebral-Cortex map to reduced label 3 -------------- Making Left-Cerebral-White-Matter map to reduced label 4 -------------- Making Left-Lateral-Ventricle map to reduced label 5 -------------- Making Left-choroid-plexus map to reduced label 6 -------------- Making Unknown map to reduced label 7 -------------- Making Left-VentralDC map to reduced label 8 -------------- Making Left-Putamen map to reduced label 9 -------------- Making Left-Pallidum map to reduced label 10 -------------- Making Left-Thalamus-Proper map to reduced label 11 -------------- Making Left-Accumbens-area map to reduced label 12 -------------- Making Left-Caudate map to reduced label 13 Error using segmentSubjectT1_autoEstimateAlveusML (line 348) The vector of prior probabilities in the mesh nodes must always sum to one over all classes

1 0

I
by Smith, Stuart 09 Sep '20

09 Sep '20

External Email - Use Caution In Get Outlook for iOyiS<https://aka.ms/o0ukef>

1 0

Extending the pial surface
by Monica Bondy 09 Sep '20

09 Sep '20

External Email - Use Caution Hi Freesurfer Developers, I was hoping to get some advice on fixing pial surface error so we can calculate cortical thickness. In several patients, although the aseg is fine, the red outline for the pial surface is missing parts of the cortex (not the subcortical areas, those are alright). Unfortunately, we cannot use control points to edit the pial surface because there is no white matter in those parts of the brain. Is it possible to manually extend the pial surface to include the excluded cortex? Also, I looked through the archive and found a similar question and read that overriding the intensity statistics that mris_make_surfaces computes automatically may solve my issue. If this is possible could I have some advice on how to do this? Otherwise, if you have any advice to fix this problem we would greatly appreciate it. Thanks, Monica

3 2

Re: [Freesurfer] Mean Gyrification index
by vittal korann 09 Sep '20

09 Sep '20

External Email - Use Caution Dear FreeSurfer experts I am working on the gyrification index of schizophrenia patients. I had collated global brain values such as thickness, GM, and WM volumes. In addition, I wanted to tabulate gyrification values. Using the below link I was able to extract the hemispheric mean gyrification values. https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31829.html But it is giving me 2 rows of output that are adding more ambiguity to the existing problem. Below is the command which I used to get mean gyrification for the left hemisphere and also the corresponding output. > *Command Line: * mri_segstats --slabel CSRI104 lh > /usr/local/freesurfer//subjects/CSRI104/label/lh.cortex --i > /usr/local/freesurfer//subjects/CSRI104/surf/lh.pial_lgi --sum > lh.aparc.pial_lgi.stats *Output: * # NRows 2 > # NTableCols 10 > # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min > Max Range > 1 0 6879 4687.8 Seg0000 2.4509 0.2838 1.8067 > 2.8873 1.0806 > 2 1 128054 84259.7 Seg0001 3.0148 0.6366 1.9369 > 4.7611 2.8242 My confusion is that which row I should take it as a mean gyrification value for the left hemisphere (seg0000 or seg0001)? Please guide me if there is a way to combine two hemispheric values and make it as mean gyrification alike mean thickness. With regards Korann On Wed, Sep 9, 2020 at 4:51 PM vittal korann <vittalkorann(a)gmail.com> wrote: > FreeSurfer experts > > I am trying to extract the mean gyrification values for the whole brain > alike cortical thickness. > We have all the whole-brain parameters in 'aparc.stats' file. But we do > not have one for the gyrification index. Is there a way to do it? > > Would be grateful for your help. > > Best > Korann > >

2 1

Freesurfer Licensing
by Rollo, Patrick 09 Sep '20

09 Sep '20

External Email - Use Caution Hi all, My group is working on a software platform with the hopes of some level of commercialization. Our platform uses some freesurfer code. Is there a specific person or group I can contact and work with to figure out the specifics of what this situation requires? Best, Patrick Rollo 713-500-5475

2 1

mri_vol2vol with --inv-morph producing unexpected results
by Noriana Jakopin 09 Sep '20

09 Sep '20

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to use the inverse of the final m3z registration file produced by mri_cvs_register to take files in mni152 space back into my subject's space. I used mri_vol2vol with the --inv-morph flag to accomplish this. However, the resulting outputs produce images with abnormal warpings to the brain. Using mri_vol2vol to take subject files into mni152 space with the same m3z file works fine, it seems to be the inverse that is the problem. Does anyone have thoughts on how I can remedy this issue? FreeSurfer Version: freesurfer-linux-centos6_x86_64-7.1.1 Platform: Windows Subsystem for Linux - Ubuntu 18.04 LTS Thank you! Noriana Jakopin

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Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all
by Park, James 09 Sep '20

09 Sep '20

External Email - Use Caution Sincerely, James Park From: "Park, James" <james.kunwoo.park(a)emory.edu> Date: Tuesday, September 8, 2020 at 11:48 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all Dear FreeSurfer Developers, We have recently been exploring the recon -all option to analyze T1 MRI data and ran into an error specifically when utilizing the -parallel flag. We specifically ran into errors at the cortical ribbon mask stage during the code we ran (shown below with some parts of the paths removed). recon-all -i “…preOp_T1MRI_axial-anon.nii" -s "freesurfer_output" -sd “…/freesurfer_output" -all -parallel When the same code was run without the -parallel flag, the recon-all line ran successfully. This was run on a Mac with macOS Catalina Version 10.15.6 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551. The recon-all.log file has been attached here as a reference. Thank you for your help in advance. Sincerely, James Park Willie Lab, Dpt. of Neurosurgery, Emory ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

2 5

runmrispreproc.sh, error
by Francesco Macchione 09 Sep '20

09 Sep '20

External Email - Use Caution we contact you for some problems in the group analysis using MrisPreproc script (freeSurfer). We followed all the instructions provided in the Andy's Brain Book, Tutorial 8. We first downloaded the shell script runmrisPreproc.sh, but when we try to run by typing "tcsh runMrisPreproc. sh ......Study" (we named our study TleStudy with two groups, HC vs TLE), two kinds of error come out. The first is "Expression Syntax" (look at the attached n.1), the second is "command not found". Thanks

2 1

Log transformation vertex-wise
by Jose Graterol 09 Sep '20

09 Sep '20

External Email - Use Caution Hello FreeSurfer Developers, I have a technical question for which I have not yet found the answer. First, I am running FreeSurfer stable-pub-v6.0.0-2beb96c on CentOS 7. Now to the question: is there a way to apply, say, a logarithmic transformation vertex-wise? For example, while doing a whole-brain analysis for cortical thickness with mri_glmfit it would calculate everything with the logarithmic value instead of mm. If this is not implemented, do you have an idea of how I could achieve this? Perhaps extracting the matrix with the values of each vertex and reading it in Matlab? Thanks in advance. José

3 4

Re: [Freesurfer] recon-all exited with errors
by Vinny K 09 Sep '20

09 Sep '20

External Email - Use Caution Hi, I've tried to process a scan but it gets hung up on a particular large defect and then exits with error. I've had large defects with other scans before but recon-all was able to get past it. How can I correct this? I've attached the recon-all log. Thanks, Vinny

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Freesurfer September 2020