recon-all -i /Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii -s sub-01 -all Adding options -fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph ERROR: cannot use ML routines (base) yanez-ramos.mariaguadalupe@r5523400 ~ % export FS_ALLOW_DEEP=1 (base) yanez-ramos.mariaguadalupe@r5523400 ~ % recon-all -i /Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii -s sub-01 -all Adding options -fix-ento-wm -transfer-base-bfs -fix-vsinus -fix-mca-dura -fix-ga -fix-acj -synthstrip -synthseg -synthmorph fs-check-version --s sub-01 --o /var/folders/16/f9gjt8xd7_v0sgpr1t4hyf3w0000gr/T//tmp.fpd295 Tue Feb 11 12:44:26 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer cd /Users/LupitaYanez /Applications/freesurfer/8.0.0-beta/bin/fs-check-version --s sub-01 --o /var/folders/16/f9gjt8xd7_v0sgpr1t4hyf3w0000gr/T//tmp.fpd295 -rwxr-xr-x 1 root wheel 18565 Nov 3 18:22 /Applications/freesurfer/8.0.0-beta/bin/fs-check-version freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc $Id$ Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 pid 99650 Current FS Version freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc Subject does not have a bstampfile, copying /Applications/freesurfer/8.0.0-beta/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer Actual FREESURFER_HOME /Applications/freesurfer/8.0.0-beta Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 \n mri_convert /Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig/001.mgz \n mri_convert /Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig/001.mgz INFO: using NIfTI-1 sform (sform_code=2) reading from /Users/LupitaYanez/Documents/Subjects/sub-01/sub-01_ses-mri01_desc-acpc_T1w_biasCorrected.nii... TR=0.00, 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) writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Feb 11 12:44:30 CST 2025 Found 1 runs /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. \n cp /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig/001.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz \n \n mri_info /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz \n rawavg.mgz ======================================== Volume information for /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz type: MGH intent: MRI (0) dimensions: 181 x 217 x 181 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 217.000 dof: 1 xstart: -90.5, xend: 90.5 ystart: -108.5, yend: 108.5 zstart: -90.5, zend: 90.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = 1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.5000 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 1.0000 0.0000 0.0000 -90.0000 0.0000 1.0000 0.0000 -126.0000 0.0000 0.0000 1.0000 -72.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 1 ras to voxel transform: 1.0000 0.0000 0.0000 90.0000 0.0000 1.0000 0.0000 126.0000 0.0000 0.0000 1.0000 72.0000 0.0000 0.0000 0.0000 1.0000 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 \n mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz --conform \n mri_convert /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz --conform reading from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz... TR=0.00, 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) volume geometry: valid : 0 extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 0.5000, -17.5000, 18.5000) file : /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 49785.6 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz... \n mri_add_xform_to_header -c /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/talairach.xfm /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz \n INFO: extension is mgz \n mri_info /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz \n orig.mgz ======================================== Volume information for /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz type: MGH intent: MRI (0) dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 1 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.5000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = -17.5000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 18.5000 talairach xfm : /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 128.5000 0.0000 0.0000 1.0000 -145.5000 0.0000 -1.0000 0.0000 146.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 128.5000 -0.0000 -0.0000 -1.0000 146.5000 -0.0000 1.0000 -0.0000 145.5000 -0.0000 -0.0000 -0.0000 1.0000 lta_convert --inlta identity.nofile --src /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz --trg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz --outlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg2orig.lta dev --inlta: identity.nofile input LTA transform. --src: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg.mgz src image (geometry). --trg: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz trg image (geometry). --outlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg2orig.lta output LTA. LTA read, type : 1 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/rawavg2orig.lta... lta_convert successful. \n mri_synthstrip --threads 1 -i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz -o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthstrip.mgz \n Configuring model on the CPU Running SynthStrip model version 1 Input image read from: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz Processing frame (of 1): 1 done Masked image saved to: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthstrip.mgz If you use SynthStrip in your analysis, please cite: ---------------------------------------------------- SynthStrip: Skull-Stripping for Any Brain Image A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann NeuroImage 206 (2022), 119474 https://doi.org/10.1016/j.neuroimage.2022.119474 Website: https://synthstrip.io \n mri_synthseg --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthseg.rca.mgz --threads 1 --vol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/stats/synthseg.vol.csv --keepgeom --addctab --cpu \n SynthSeg 2.0 using CPU, hiding all CUDA_VISIBLE_DEVICES using 1 thread addctab True predicting 1/1 1/1 [==============================] - 324s 324s/step Reslicing to have same geom as the input [1. 1. 1.] segmentation saved in: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthseg.rca.mgz volumes saved in: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/stats/synthseg.vol.csv #@# mri_synthseg vmpeak None If you use this tool in a publication, please cite: SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining B. Billot, D.N. Greve, O. Puonti, A. Thielscher, K. Van Leemput, B. Fischl, A.V. Dalca, J.E. Iglesias Medical Image Analysis, 2023. ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 csvprint: Command not found. ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 Tue Feb 11 12:51:17 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 /Applications/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthstrip.mgz --t /Applications/freesurfer/8.0.0-beta/average/mni305.cor.stripped.mgz --affine-only --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305 --threads 1 -rwxr-xr-x 1 root wheel 30900 Nov 3 18:25 /Applications/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc $Id$ Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 pid 242 Tue Feb 11 12:51:17 CST 2025 \n\n mri_synthmorph -m affine -t /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/aff.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthstrip.mgz /Applications/freesurfer/8.0.0-beta/average/mni305.cor.stripped.mgz -j 1 Thank you for choosing SynthMorph. Please cite us! SynthMorph: learning contrast-invariant registration without acquired images Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022 https://doi.org/10.1109/TMI.2021.3116879 Anatomy-specific acquisition-agnostic affine registration learned from fictitious images Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution) SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023 https://doi.org/10.1117/12.2653251 https://synthmorph.io/#papers (PDF) Anatomy-aware and acquisition-agnostic joint registration with SynthMorph Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution) Imaging Neuroscience, 2, 1-33, 2024 https://doi.org/10.1162/imag_a_00197 Website: https://synthmorph.io ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305 ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 lta_convert --invert --inlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/aff.lta --outlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta dev --invert: will invert transform. --inlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/aff.lta input LTA transform. --outlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta output LTA. LTA read, type : 1 1.08684 0.08641 0.04272 -2.30560; -0.05741 1.05093 -0.07044 -2.13585; 0.01811 -0.01467 1.21110 -3.66046; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/reg.targ_to_invol.lta... lta_convert successful. \n\n To check affine registration tkregisterfv --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/synthstrip.mgz --targ /Applications/freesurfer/8.0.0-beta/average/mni305.cor.stripped.mgz --reg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.mni305/aff.lta AffineOnly specified, so exiting now Started at Tue Feb 11 12:51:17 CST 2025 Ended at Tue Feb 11 12:52:00 CST 2025 Fs-Synthmorph-Reg-Run-Time-Sec 43 Fs-Synthmorph-Reg-Run-Time-Min 0.72 Fs-Synthmorph-Reg-Run-Time-Hours 0.01 fs-synthmorph-reg Done ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 dev --ltavox2vox: output LTA as VOX_TO_VOX transform. --inlta: synthmorph.mni305/aff.lta input LTA transform. --outlta: talairach.xfm.lta output LTA. LTA read, type : 1 1.08684 0.08641 0.04272 -2.30560; -0.05741 1.05093 -0.07044 -2.13585; 0.01811 -0.01467 1.21110 -3.66046; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file talairach.xfm.lta... lta_convert successful. dev --inlta: talairach.xfm.lta input LTA transform. --outmni: talairach.xfm output MNI/XFM matrix. LTA read, type : 1 1.08684 0.08641 0.04272 -2.30562; -0.05741 1.05093 -0.07044 -2.13585; 0.01811 -0.01467 1.21110 -3.66046; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 \n fs-synthmorph-reg --s sub-01 --threads 1 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz --test \n Tue Feb 11 12:52:00 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01 /Applications/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg --s sub-01 --threads 1 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz --test -rwxr-xr-x 1 root wheel 30900 Nov 3 18:25 /Applications/freesurfer/8.0.0-beta/bin/fs-synthmorph-reg freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc $Id$ Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 pid 566 mri_mask -bb 3 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz cropping npad = 3 DoAbs = 0 Computing bounding box, npad = 3, 3, 3, 3, 3, 3 35 35 16 180 187 223 maskval=0, outval=0 Writing masked volume to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz...done. lta_convert --inlta identity.nofile --src /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --trg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz --outlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta dev --inlta: identity.nofile input LTA transform. --src: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz src image (geometry). --trg: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz trg image (geometry). --outlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta output LTA. LTA read, type : 1 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta... lta_convert successful. Tue Feb 11 12:52:01 CST 2025 \n\n mri_synthmorph -m affine -t /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 1 [DEBUG] FSNifti1Extension.read(): esize = 1520 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1508 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1492 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1453 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1393 (tag = 31, length = 131) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1250 (tag = 3, length = 595) [DEBUG] FSNifti1Extension.read(): remaining taglen = 643 (tag = 3, length = 610) [DEBUG] FSNifti1Extension.read(): remaining taglen = 21 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 8 [DEBUG] FSNifti1Extension.read(): esize = 144 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 132 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 116 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 77 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 17 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 4 Thank you for choosing SynthMorph. Please cite us! SynthMorph: learning contrast-invariant registration without acquired images Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022 https://doi.org/10.1109/TMI.2021.3116879 Anatomy-specific acquisition-agnostic affine registration learned from fictitious images Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution) SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023 https://doi.org/10.1117/12.2653251 https://synthmorph.io/#papers (PDF) Anatomy-aware and acquisition-agnostic joint registration with SynthMorph Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution) Imaging Neuroscience, 2, 1-33, 2024 https://doi.org/10.1162/imag_a_00197 Website: https://synthmorph.io Tue Feb 11 12:52:37 CST 2025 \n\n mri_concatenate_lta -invert1 -invertout /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta invert the first LTA before applying it invert the output LTA Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Inverting output LTA Writing combined LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta... mri_concatenate_lta successful. \n\n mri_concatenate_lta -invert2 /Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.to.1.0mm.cropped.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.invol_to_croptarg.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert the second LTA before applying it Read individual LTAs Combining the two LTAs to get a RAS-to-RAS from src of LTA1 to dst of LTA2... Writing combined LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta... mri_concatenate_lta successful. \n\n lta_convert --invert --inlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --outlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta dev --invert: will invert transform. --inlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta input LTA transform. --outlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta output LTA. LTA read, type : 1 0.87815 -0.06784 -0.04863 2.87647; 0.03993 0.91526 0.09739 1.04553; -0.00669 0.01654 0.78237 3.06534; 0.00000 0.00000 0.00000 1.00000; Writing LTA to file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta... lta_convert successful. \n\n lta_convert --inlta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta --outmni /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm dev --inlta: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta input LTA transform. --outmni: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.xfm output MNI/XFM matrix. LTA read, type : 1 1.13544 0.08307 0.06023 -3.53753; -0.05069 1.09134 -0.13900 -0.56914; 0.01077 -0.02236 1.28161 -3.93619; 0.00000 0.00000 0.00000 1.00000; lta_convert successful. \n\n To check affine registration tkregisterfv --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz --targ /Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --reg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.invol_to_targ.lta \n\n mri_synthmorph -m deform -t /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz -i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/aff.lta /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz /Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.cropped.nii.gz -j 1 -o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz [DEBUG] FSNifti1Extension.read(): esize = 1520 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1508 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1492 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1453 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1393 (tag = 31, length = 131) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1250 (tag = 3, length = 595) [DEBUG] FSNifti1Extension.read(): remaining taglen = 643 (tag = 3, length = 610) [DEBUG] FSNifti1Extension.read(): remaining taglen = 21 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 8 [DEBUG] FSNifti1Extension.read(): esize = 144 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 132 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 116 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 77 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 17 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 4 Thank you for choosing SynthMorph. Please cite us! SynthMorph: learning contrast-invariant registration without acquired images Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022 https://doi.org/10.1109/TMI.2021.3116879 Anatomy-specific acquisition-agnostic affine registration learned from fictitious images Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution) SPIE Medical Imaging: Image Processing, 12464, 1246402, 2023 https://doi.org/10.1117/12.2653251 https://synthmorph.io/#papers (PDF) Anatomy-aware and acquisition-agnostic joint registration with SynthMorph Hoffmann M, Hoopes A, Greve DN, Fischl B*, Dalca AV* (*equal contribution) Imaging Neuroscience, 2, 1-33, 2024 https://doi.org/10.1162/imag_a_00197 Website: https://synthmorph.io \n\nmri_warp_convert --inras /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz --insrcgeom /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz --outm3z /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz --vg-thresh 1e-5 --lta1-inv /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/reg.crop-to-invol.lta --lta2 /Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/reg.1.0mm.cropped.to.1.0mm.lta dev --inras: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/deform.mgz input RAS warp. --insrcgeom: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/invol.crop.nii.gz atlas/source image (used for geometry). --outm3z: /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz output M3Z. Setting vg_isEqual_Threshold to 0.000010 Applying LTAs to the GCAM GCAMwrite(/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz) [INFO] Warpfield::convert(): converting GCAM ... [INFO] Warpfield::convert(): gcam [193 x 229 x 193] [INFO] Warpfield::convert(): gcam image [256 x 256 x 256] [INFO] Warpfield::convert(): gcam atlas [193 x 229 x 193] [INFO] Warpfield::convert(): total out of range voxel count: 0 volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 0.5000, -17.5000, 18.5000) file : /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz volume geometry: extent : (193, 229, 193) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : ( 1.0000, -0.0000, 0.0000) y_(ras) : (-0.0000, 1.0000, 0.0000) z_(ras) : (-0.0000, -0.0000, 1.0000) c_(ras) : ( 0.5000, -17.5000, 18.5000) file : /autofs/space/curv_001/users/fs-mni152-atlas/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz mri_warp_convert successful. \n\nmri_ca_register -invert-and-save /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz INFO: using NIfTI-1 sform (sform_code=1) Loading gcam [DEBUG] Warpfield::read() gcam->status = GCAM_LABELED setting orig areas to linear transform determinant scaled 1.00 Computing inverse of GCAM Filling inverse of GCAM Allocating inv_gcam...(256, 256, 256) Saving inverse to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz GCAMwrite(/Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.inv.nii.gz) [INFO] Warpfield::convert(): converting GCAM ... [INFO] Warpfield::convert(): gcam [256 x 256 x 256] [INFO] Warpfield::convert(): gcam image [193 x 229 x 193] [INFO] Warpfield::convert(): gcam atlas [256 x 256 x 256] [INFO] Warpfield::convert(): total out of range voxel count: 0 volume geometry: extent : (193, 229, 193) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : ( 1.0000, -0.0000, 0.0000) y_(ras) : (-0.0000, 1.0000, 0.0000) z_(ras) : (-0.0000, -0.0000, 1.0000) c_(ras) : ( 0.5000, -17.5000, 18.5000) file : /autofs/space/curv_001/users/fs-mni152-atlas/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, 0.0000, 0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : ( 0.0000, 1.0000, 0.0000) c_(ras) : ( 0.5000, -17.5000, 18.5000) file : /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz mri_vol2vol --regheader --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz --targ /Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz movvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/synthmorph.out.mgz targvol /Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1740048430 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -0.50000; 0.00000 1.00000 0.00000 13.50000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 -20.00000; 0.00000 1.00000 0.00000 -20.00000; 0.00000 0.00000 1.00000 -2.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_convert -rt nearest /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz -at /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz mri_convert -rt nearest /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.mgz -at /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz INFO: using NIfTI-1 sform (sform_code=1) reading from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/orig.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) INFO: Reading transformation from file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... INFO: Applying transformation from file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/warp.to.mni152.1.0mm.1.0mm.nii.gz... Applying morph_3d ... [DEBUG] Warpfield::read() gcam->status = GCAM_LABELED setting orig areas to linear transform determinant scaled 1.00 morphing to atlas with resample type 0 writing to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz... mri_diff --po /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz mri_diff --po /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/tmp/morph.out.nii.gz diffcount 4338064 Volumes differ in pixel data maxdiff 108.62528229 at 64 177 128 0 tkmeditfv -f /Applications/freesurfer/8.0.0-beta/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz -aux /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/test.nii.gz Started at Tue Feb 11 12:52:00 CST 2025 Ended at Tue Feb 11 13:10:06 CST 2025 Fs-Synthmorph-Reg-Run-Time-Sec 1085 Fs-Synthmorph-Reg-Run-Time-Min 18.08 Fs-Synthmorph-Reg-Run-Time-Hours 0.30 fs-synthmorph-reg Done #-------------------------------------------- #@# Nu Intensity Correction Tue Feb 11 13:10:06 CST 2025 \n mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 \n /usr/bin/bc /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri /Applications/freesurfer/8.0.0-beta/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 FreeSurferEnv.csh dev Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 Tue Feb 11 13:10:06 CST 2025 tmpdir is ./tmp.mri_nu_correct.mni.1514 cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.1514/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.1514/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.1514/ones.mgz dev cwd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.1514/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.1514/ones.mgz sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe input ./tmp.mri_nu_correct.mni.1514/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.1514/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.1514/ones.mgz Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1514/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1514/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1514/input.mean.dat dev cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1514/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.1514/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1514/input.mean.dat sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1514/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.1514/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1514/ones.mgz --i ./tmp.mri_nu_correct.mni.1514/nu0.mgz --sum ./tmp.mri_nu_correct.mni.1514/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1514/output.mean.dat dev cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1514/ones.mgz --i ./tmp.mri_nu_correct.mni.1514/nu0.mgz --sum ./tmp.mri_nu_correct.mni.1514/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1514/output.mean.dat sysname Darwin hostname r5523400.mayo.edu machine arm64 user yanez-ramos.mariaguadalupe whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1514/ones.mgz Loading ./tmp.mri_nu_correct.mni.1514/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.1514/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.1514/nu0.mgz ./tmp.mri_nu_correct.mni.1514/nu0.mgz mul 1.13345000013348604136 Packing Done packing Unpacking Saving result to './tmp.mri_nu_correct.mni.1514/nu0.mgz' (type = MGH ) [ ok ] #VMPC# mris_calc VmPeak 0 mri_convert ./tmp.mri_nu_correct.mni.1514/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.1514/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.1514/nu0.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) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 1 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 5, i2 = 71 #mri_make_uchar# mapping 12 167 to 3 110 : b -5.59015 m 0.691738 : thresh 8.08131 maxsat 376.718 : nzero 13848606 nsat 0 Tue Feb 11 13:10:51 CST 2025 mri_nu_correct.mni done \n mri_add_xform_to_header -c /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/talairach.xfm nu.mgz nu.mgz \n INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Feb 11 13:10:51 CST 2025 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri \n mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz \n using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... normalizing image... NOT doing gentle normalization with control points/label talairach transform 1.08684 0.08641 0.04272 -2.30562; -0.05741 1.05093 -0.07044 -2.13585; 0.01811 -0.01467 1.21110 -3.66046; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 22 Starting OpenSpline(): npoints = 22 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 68 (68), valley at 32 (32) csf peak at 10, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 68 (68), valley at 31 (31) csf peak at 10, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 0 minutes and 44 seconds. #-------------------------------------- \n#@# MCADura Segmentation Tue Feb 11 13:11:36 CST 2025 mri_mcadura_seg --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/nu.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/mca-dura.mgz --threads 1 --synthmorphdir /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm Tue Feb 11 13:11:36 CST 2025 setenv SUBJECTS_DIR /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer cd /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri /Applications/freesurfer/8.0.0-beta/bin/mri_mcadura_seg --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/nu.mgz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/mca-dura.mgz --threads 1 --synthmorphdir /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm -rwxr-xr-x 1 root wheel 13384 Nov 3 18:22 /Applications/freesurfer/8.0.0-beta/bin/mri_mcadura_seg freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc $Id$ Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 pid 1718 ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718 ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri ~/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri mri_vol2vol --reg /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta --mov /Applications/freesurfer/8.0.0-beta/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/mcadura.prior.lh.nii.gz regio_read_register: loading lta Matrix from regfile: -1.13544 -0.08307 -0.06023 3.80927; 0.01077 -0.02236 1.28161 1.67021; 0.05069 -1.09134 0.13900 4.76448; 0.00000 0.00000 0.00000 1.00000; Getting target volume geom from lta destination movvol /Applications/freesurfer/8.0.0-beta/average/mca-dura.prior.warp.mni152.1.0mm.lh.nii.gz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/mcadura.prior.lh.nii.gz regfile /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/transforms/synthmorph.1.0mm.1.0mm/reg.targ_to_invol.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1739881588 Final tkRAS-to-tkRAS Matrix is: -1.13544 -0.08307 -0.06023 3.80927; 0.01077 -0.02236 1.28161 1.67021; 0.05069 -1.09134 0.13900 4.76448; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: -1.13544 -0.06023 0.08307 235.10382; 0.05069 0.13900 1.09134 -54.23622; -0.01077 -1.28161 -0.02236 266.45721; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_mask -T .001 -crop-to-fov-mm 80 80 80 /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/nu.mgz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/mcadura.prior.lh.nii.gz /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/lh.crop.nii.gz threshold mask volume at 0.001 CropToFoVmm 80 80 80 DoAbs = 0 Found 5557 voxels in mask (pct= 0.03) MRIcropToFoV(): thresh=0.001 FoV = (80,80,80) nhits=5557 centroid = (161.479,159.884,163.755) min = (134,139,147) max = (181,177,179) delta = (48,39,33) Region 121 120 124 80 80 80 121 120 124 80 80 80 maskval=0, outval=0 Writing masked volume to /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/lh.crop.nii.gz...done. mri_vol2vol --regheader --mov /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/nu.mgz --targ /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/lh.crop.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/invol.lh.crop.nii.gz movvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/nu.mgz targvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/lh.crop.nii.gz outvol /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/invol.lh.crop.nii.gz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1739537718 Computing registration based on scanner-to-scanner Final tkRAS-to-tkRAS Matrix is: 1.00000 0.00000 0.00000 -33.00000; 0.00000 1.00000 0.00000 36.00000; 0.00000 0.00000 1.00000 -32.00000; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.00000 0.00000 0.00000 121.00000; 0.00000 1.00000 0.00000 120.00000; 0.00000 0.00000 1.00000 124.00000; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done mri_sclimbic_seg --model /Applications/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/invol.lh.crop.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/seg.lh.mgz Traceback (most recent call last): File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 1073, in /Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg --model /Applications/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 --ctab /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/dumca.lh.ctab --keep_ac --percentile 99.9 --vmp --output-base mcadura --conform --logfile mri_mcadura_seg.log --no-cite-sclimbic --threads 1 --fov 72 --i /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/invol.lh.crop.nii.gz --o /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/seg.lh.mgz Keeping anterior commissure in vols and stats Using CPU Using 1 thread(s) Loaded lookup table /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/dumca.lh.ctab Loaded population stats /Applications/freesurfer/8.0.0-beta/models/sclimbic.volstats.csv nb_labels 2 inshape (72, 72, 72) features 24 (None, 72, 72, 72, 1) Loading weights from /Applications/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 ----------------------- Done loading weights ----------------------- Loaded model weights /Applications/freesurfer/8.0.0-beta/models/mca-dura.both-lh.nstd21.fhs.h5 Segmenting image 1/1 [DEBUG] FSNifti1Extension.read(): esize = 1520 [DEBUG] FSNifti1Extension.read(): endian = '>', intent = 0, version = 1 [DEBUG] FSNifti1Extension.read(): remaining taglen = 1508 (tag = 7, length = 4) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1492 (tag = 45, length = 27) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1453 (tag = 8, length = 48) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1393 (tag = 31, length = 131) [DEBUG] FSNifti1Extension.read(): remaining taglen = 1250 (tag = 3, length = 595) [DEBUG] FSNifti1Extension.read(): remaining taglen = 643 (tag = 3, length = 610) [DEBUG] FSNifti1Extension.read(): remaining taglen = 21 (tag = -1, length = 1) [DEBUG] FSNifti1Extension.read(): remaining taglen = 8 Loaded input image from /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/mri/tmp.mri_mcadura_seg.1718/invol.lh.crop.nii.gz main() File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 324, in main segmenter.process_files(**params) File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 602, in process_files post, seg, vox_counts, volumes, mean_probs = self.segment(image) File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 524, in segment prediction = self.model.predict(conformed.framed_data[np.newaxis]).squeeze() File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 70, in error_handler raise e.with_traceback(filtered_tb) from None File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/tensorflow/python/eager/execute.py", line 53, in quick_execute tensors = pywrap_tfe.TFE_Py_Execute(ctx._handle, device_name, op_name, tensorflow.python.framework.errors_impl.InvalidArgumentError: Graph execution error: Detected at node 'unet/unet_bn_down_0/FusedBatchNormV3' defined at (most recent call last): File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 1073, in main() File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 324, in main segmenter.process_files(**params) File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 602, in process_files post, seg, vox_counts, volumes, mean_probs = self.segment(image) File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 524, in segment prediction = self.model.predict(conformed.framed_data[np.newaxis]).squeeze() File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2554, in predict tmp_batch_outputs = self.predict_function(iterator) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2341, in predict_function return step_function(self, iterator) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2327, in step_function outputs = model.distribute_strategy.run(run_step, args=(data,)) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2315, in run_step outputs = model.predict_step(data) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2283, in predict_step return self(x, training=False) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 569, in __call__ return super().__call__(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/base_layer.py", line 1150, in __call__ outputs = call_fn(inputs, *args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 96, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/functional.py", line 512, in call return self._run_internal_graph(inputs, training=training, mask=mask) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/functional.py", line 669, in _run_internal_graph outputs = node.layer(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/base_layer.py", line 1150, in __call__ outputs = call_fn(inputs, *args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 96, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/layers/normalization/batch_normalization.py", line 597, in call outputs = self._fused_batch_norm( File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/layers/normalization/batch_normalization.py", line 990, in _fused_batch_norm output, mean, variance = control_flow_util.smart_cond( File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/control_flow_util.py", line 108, in smart_cond return tf.__internal__.smart_cond.smart_cond( File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/layers/normalization/batch_normalization.py", line 979, in _fused_batch_norm_inference return tf.compat.v1.nn.fused_batch_norm( Node: 'unet/unet_bn_down_0/FusedBatchNormV3' Detected at node 'unet/unet_bn_down_0/FusedBatchNormV3' defined at (most recent call last): File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 1073, in main() File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 324, in main segmenter.process_files(**params) File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 602, in process_files post, seg, vox_counts, volumes, mean_probs = self.segment(image) File "/Applications/freesurfer/8.0.0-beta/python/scripts/mri_sclimbic_seg", line 524, in segment prediction = self.model.predict(conformed.framed_data[np.newaxis]).squeeze() File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2554, in predict tmp_batch_outputs = self.predict_function(iterator) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2341, in predict_function return step_function(self, iterator) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2327, in step_function outputs = model.distribute_strategy.run(run_step, args=(data,)) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2315, in run_step outputs = model.predict_step(data) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 2283, in predict_step return self(x, training=False) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/training.py", line 569, in __call__ return super().__call__(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/base_layer.py", line 1150, in __call__ outputs = call_fn(inputs, *args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 96, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/functional.py", line 512, in call return self._run_internal_graph(inputs, training=training, mask=mask) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/functional.py", line 669, in _run_internal_graph outputs = node.layer(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 65, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/engine/base_layer.py", line 1150, in __call__ outputs = call_fn(inputs, *args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/traceback_utils.py", line 96, in error_handler return fn(*args, **kwargs) File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/layers/normalization/batch_normalization.py", line 597, in call outputs = self._fused_batch_norm( File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/layers/normalization/batch_normalization.py", line 990, in _fused_batch_norm output, mean, variance = control_flow_util.smart_cond( File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/utils/control_flow_util.py", line 108, in smart_cond return tf.__internal__.smart_cond.smart_cond( File "/Applications/freesurfer/8.0.0-beta/python/miniconda3_apple_dist/py3_8_13/lib/python3.8/site-packages/keras/src/layers/normalization/batch_normalization.py", line 979, in _fused_batch_norm_inference return tf.compat.v1.nn.fused_batch_norm( Node: 'unet/unet_bn_down_0/FusedBatchNormV3' 2 root error(s) found. (0) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] [[unet/unet_bn_down_0/FusedBatchNormV3/_16]] (1) INVALID_ARGUMENT: input must be 4-dimensional[1,72,72,72,24] [[{{node unet/unet_bn_down_0/FusedBatchNormV3}}]] 0 successful operations. 0 derived errors ignored. [Op:__inference_predict_function_1146] ERROR: Darwin r5523400.mayo.edu 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan 2 20:24:22 PST 2025; root:xnu-11215.81.4~3/RELEASE_ARM64_T6041 arm64 recon-all -s sub-01 exited with ERRORS at Tue Feb 11 13:12:04 CST 2025 For more details, see the log file /Users/LupitaYanez/Documents/GitLabMayo/visual_connectivity/data/derivatives/freesurfer/sub-01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting