External Email - Use Caution Dear FreeSurfer experts,
I am trying to process some newborn subjects including the segfile. In both situations, including the mask file and using the --forceskullstrip flag I get the following error (log file attached): *lta_convert successful./home/fernanda/Documentos/dHCP/freesurfer1 ERROR: Option --noverbose unknown* This is the exact command I am running: *infant_recon_all --s sub-CC00060XX03 --age 0 --segfile sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz --forceskulltrip --force* How can I overcome this? Thank you very much. Fernanda Hansen P. de Moraes fernandahmor...@gmail.com Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino
Logfile for infant_recon_all ter jun 22 11:56:53 -03 2021 --s sub-CC00060XX03 --age 0 --segfile sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz --forceskullstrip --force --usegpu --intnormFSL infant_recon_all infant-dev-4a14499 computador Linux computador 4.15.0-140-generic #144-Ubuntu SMP Fri Mar 19 14:12:35 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux INPUT FILE /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/mprage.nii.gz fslmaths /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/mprage.nii.gz -div 78.578468 -mul 255 /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.nii.gz -odt char INTENSITY NORMALIZED FILE /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.nii.gz mri_convert --conform-dc /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.nii.gz /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.nii.gz mri_convert.bin --conform-dc /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.nii.gz /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (-0, -0, 1) keeping DC 0 2 1 ostr LAS, width 256, size 1 K --------------- 0.50000 0.00000 0.00000 56.00000; 0.00000 0.00000 -0.50000 178.00000; 0.00000 0.50000 0.00000 56.00000; 0.00000 0.00000 0.00000 1.00000; Kinv --------------- 2.00000 0.00000 0.00000 -112.00000; 0.00000 0.00000 2.00000 -112.00000; 0.00000 -2.00000 0.00000 356.00000; 0.00000 0.00000 0.00000 1.00000; Smri --------------- -0.50000 0.00000 -0.00000 62.93332; 0.00000 0.50000 -0.00000 -54.42529; 0.00000 0.00000 0.50000 -35.40189; 0.00000 0.00000 0.00000 1.00000; Stemp --------------- -1.00000 0.00000 0.00000 118.93332; 0.00000 0.00000 1.00000 -110.42529; 0.00000 -1.00000 0.00000 142.59811; 0.00000 0.00000 0.00000 1.00000; ---------------------- changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.nii.gz... CONFORMED FILE /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.nii.gz sscnn_skullstrip -i /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.nii.gz -o /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/sscnn -c t1w --gpu -1 2021-06-22 11:56:57.202913: I tensorflow/core/platform/cpu_feature_guard.cc:137] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA Using TensorFlow backend. /usr/local/freesurfer/python/scripts/sscnn_skullstrip:93: UserWarning: The argument 'neighbors' is deprecated and will be removed in scikit-image 0.18, use 'connectivity' instead. For neighbors=8, use connectivity=3 label_img_data = skimage.measure.label(np.int8(hard_img_data), neighbors=8) mri_convert.bin --conform /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.nii.gz /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/sscnn/conformed.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/sscnn/conformed.nii.gz... [<tf.Tensor 'bnorm_D_1_00_1/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_01_1/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_10_1/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_11_1/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_20_1/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_21_1/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_30_1/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_31_1/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_40_1/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_41_1/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_50_1/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>, <tf.Tensor 'bnorm_D_1_51_1/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>] 12 Loaded model file: /usr/local/freesurfer/average/sscnn_skullstripping/cor_sscnn.h5 1.624203821656051 Image max is :1.624203821656051 [<tf.Tensor 'bnorm_D_1_00_3/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_01_3/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_10_3/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_11_3/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_20_3/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_21_3/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_30_3/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_31_3/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_40_3/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_41_3/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_50_3/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>, <tf.Tensor 'bnorm_D_1_51_3/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>] 12 Loaded model file: /usr/local/freesurfer/average/sscnn_skullstripping/ax_sscnn.h5 1.624203821656051 Image max is :1.624203821656051 [<tf.Tensor 'bnorm_D_1_00_5/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_01_5/cond/Merge:0' shape=(?, 256, 256, 32) dtype=float32>, <tf.Tensor 'bnorm_D_1_10_5/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_11_5/cond/Merge:0' shape=(?, 128, 128, 64) dtype=float32>, <tf.Tensor 'bnorm_D_1_20_5/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_21_5/cond/Merge:0' shape=(?, 64, 64, 128) dtype=float32>, <tf.Tensor 'bnorm_D_1_30_5/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_31_5/cond/Merge:0' shape=(?, 32, 32, 256) dtype=float32>, <tf.Tensor 'bnorm_D_1_40_5/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_41_5/cond/Merge:0' shape=(?, 16, 16, 512) dtype=float32>, <tf.Tensor 'bnorm_D_1_50_5/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>, <tf.Tensor 'bnorm_D_1_51_5/cond/Merge:0' shape=(?, 8, 8, 1024) dtype=float32>] 12 Loaded model file: /usr/local/freesurfer/average/sscnn_skullstripping/sag_sscnn.h5 1.624203821656051 Image max is :1.624203821656051 mv /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/sscnn/sscnn_skullstrip.nii.gz /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.mask.nii.gz MASK FILE /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.mask.nii.gz mri_mask /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.nii.gz /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.mask.nii.gz /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.masked.nii.gz DoAbs = 0 Writing masked volume to /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.masked.nii.gz...done. MASKED FILE /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.masked.nii.gz MASKED FILE /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.masked.nii.gz WORKING WITH EXISTING SEGMENTATION FILE sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz mri_convert --conform-dc sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/finalaseg.nii.gz -rt nearest --no_scale 1 mri_convert.bin --conform-dc sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/finalaseg.nii.gz -rt nearest --no_scale 1 INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sub-CC00060XX03/sub-CC00060XX03_ses-12501_desc-drawem87_space-T2w_dseg.nii.gz... TR=1.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (-0, -0, 1) keeping DC 0 2 1 ostr LAS, width 256, size 1 K --------------- 0.50000 0.00000 0.00000 56.00000; 0.00000 0.00000 -0.50000 178.00000; 0.00000 0.50000 0.00000 56.00000; 0.00000 0.00000 0.00000 1.00000; Kinv --------------- 2.00000 0.00000 0.00000 -112.00000; 0.00000 0.00000 2.00000 -112.00000; 0.00000 -2.00000 0.00000 356.00000; 0.00000 0.00000 0.00000 1.00000; Smri --------------- -0.50000 0.00000 -0.00000 62.93332; 0.00000 0.50000 -0.00000 -54.42529; 0.00000 0.00000 0.50000 -35.40189; 0.00000 0.00000 0.00000 1.00000; Stemp --------------- -1.00000 0.00000 0.00000 118.93332; 0.00000 0.00000 1.00000 -110.42529; 0.00000 -1.00000 0.00000 142.59811; 0.00000 0.00000 0.00000 1.00000; ---------------------- changing data type from float to uchar (noscale = 1)... Reslicing using nearest writing to /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/finalaseg.nii.gz... mkdir -p /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms mkdir -p /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/surf mkdir -p /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/label mkdir -p /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/stats cp /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.masked.nii.gz norm.nii.gz mri_convert norm.nii.gz norm.mgz mri_convert.bin norm.nii.gz norm.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from norm.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to norm.mgz... ln -s norm.nii.gz brain.nii.gz ln -s norm.mgz brain.mgz ln -s norm.nii.gz brainmask.nii.gz ln -s norm.mgz brainmask.mgz cp /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/finalaseg.nii.gz aseg.nii.gz mri_convert aseg.nii.gz aseg.mgz mri_convert.bin aseg.nii.gz aseg.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from aseg.nii.gz... TR=1.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to aseg.mgz... mri_convert /usr/local/freesurfer/average/mni305.cor.mgz ./mni305.cor.nii.gz mri_convert.bin /usr/local/freesurfer/average/mni305.cor.mgz ./mni305.cor.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /usr/local/freesurfer/average/mni305.cor.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./mni305.cor.nii.gz... reg_aladin -ref ./mni305.cor.nii.gz -flo /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.masked.nii.gz -aff /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/niftyreg_affine.txt -res /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/niftyreg_affine.nii.gz -voff Padding value here nan lta_convert --inniftyreg /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/niftyreg_affine.txt --outlta /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/niftyreg_affine.lta --outmni /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/niftyreg_affine.xfm --src /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.masked.nii.gz --trg ./mni305.cor.nii.gz $Id: lta_convert.cpp,v 1.9.2.1 2016/08/09 02:33:22 zkaufman Exp $ --inniftyreg: /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/niftyreg_affine.txt input Nifty Reg transform. --outlta: /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/niftyreg_affine.lta output LTA. --outmni: /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/niftyreg_affine.xfm output MNI/XFM matrix. --src: /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work/mprage_fslnorm.conf.masked.nii.gz src image (geometry). --trg: ./mni305.cor.nii.gz trg image (geometry). LTA read, type : 1 1.75343 -0.05026 0.00297 18.01541; 0.12790 1.72997 0.41607 -54.83729; -0.04414 -0.35722 1.78517 -18.39733; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/niftyreg_affine.lta... lta_convert successful. rm -f ./mni305.cor.nii.gz cp /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/niftyreg_affine.xfm /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/talairach.auto.xfm cp /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/talairach.auto.xfm /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/transforms/talairach.xfm mri_binarize --match 2 41 --count /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/aseg.count.txt --i /home/fernanda/Documentos/dHCP/freesurfer1/sub-CC00060XX03/work//sub-CC00060XX03/mri/aseg.nii.gz --noverbose ERROR: Option --noverbose unknown
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