recon-all -i /flywheel/v0/input/anatomical/T1w_MPR.nii.gz -subjid 05 -debug -all -qcache -openmp 4 -openmp 2 fs-check-version --s 05 --o /tmp/tmp.mwcGuM Thu Sep 4 18:06:35 UTC 2025 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects cd /flywheel/v0 /usr/local/freesurfer/bin/fs-check-version --s 05 --o /tmp/tmp.mwcGuM -rwxrwxr-x 1 root root 18565 Jun 14 2023 /usr/local/freesurfer/bin/fs-check-version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 $Id$ Linux 702840b9e5e3 6.8.0-1017-gcp #19-Ubuntu SMP Tue Oct 15 19:02:59 UTC 2024 x86_64 GNU/Linux pid 34 Current FS Version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /usr/local/freesurfer/build-stamp.txt Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux 702840b9e5e3 6.8.0-1017-gcp #19-Ubuntu SMP Tue Oct 15 19:02:59 UTC 2024 x86_64 GNU/Linux /usr/local/freesurfer/subjects/05 mri_convert /flywheel/v0/input/anatomical/T1w_MPR.nii.gz /usr/local/freesurfer/subjects/05/mri/orig/001.mgz mri_convert /flywheel/v0/input/anatomical/T1w_MPR.nii.gz /usr/local/freesurfer/subjects/05/mri/orig/001.mgz reading from /flywheel/v0/input/anatomical/T1w_MPR.nii.gz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.996215, -0.0738526, -0.0458488) j_ras = (0.0776606, 0.993111, 0.0877416) k_ras = (0.039053, -0.0909701, 0.995088) writing to /usr/local/freesurfer/subjects/05/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Sep 4 18:06:43 UTC 2025 Found 1 runs /usr/local/freesurfer/subjects/05/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. cp /usr/local/freesurfer/subjects/05/mri/orig/001.mgz /usr/local/freesurfer/subjects/05/mri/rawavg.mgz mri_info /usr/local/freesurfer/subjects/05/mri/rawavg.mgz rawavg.mgz ======================================== Volume information for /usr/local/freesurfer/subjects/05/mri/rawavg.mgz type: MGH dimensions: 208 x 300 x 320 voxel sizes: 0.800000, 0.800000, 0.800000 type: SHORT (4) fov: 256.000 dof: 1 xstart: -83.2, xend: 83.2 ystart: -120.0, yend: 120.0 zstart: -128.0, zend: 128.0 TR: 2400.00 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 = 0.9962, y_r = 0.0777, z_r = 0.0391, c_r = 3.3444 : x_a = -0.0739, y_a = 0.9931, z_a = -0.0910, c_a = 1.4260 : x_s = -0.0458, y_s = 0.0877, z_s = 0.9951, c_s = 7.0804 talairach xfm : Orientation : RAS Primary Slice Direction: axial voxel to ras transform: 0.7970 0.0621 0.0312 -93.8588 -0.0591 0.7945 -0.0728 -99.9587 -0.0367 0.0702 0.7961 -127.0052 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant 0.512 ras to voxel transform: 1.2453 -0.0923 -0.0573 100.3728 0.0971 1.2414 0.1097 147.1286 0.0488 -0.1137 1.2439 151.1919 0.0000 0.0000 0.0000 1.0000 /usr/local/freesurfer/subjects/05 mri_convert /usr/local/freesurfer/subjects/05/mri/rawavg.mgz /usr/local/freesurfer/subjects/05/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/05/mri/rawavg.mgz /usr/local/freesurfer/subjects/05/mri/orig.mgz --conform reading from /usr/local/freesurfer/subjects/05/mri/rawavg.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.996215, -0.0738526, -0.0458488) j_ras = (0.0776606, 0.993111, 0.0877416) k_ras = (0.039053, -0.0909701, 0.995088) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 4095 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/05/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/05/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/05/mri/orig.mgz /usr/local/freesurfer/subjects/05/mri/orig.mgz INFO: extension is mgz mri_info /usr/local/freesurfer/subjects/05/mri/orig.mgz orig.mgz ======================================== Volume information for /usr/local/freesurfer/subjects/05/mri/orig.mgz type: MGH 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: 2400.00 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 = 3.3444 : x_a = 0.0000, y_a = -0.0000, z_a = 1.0000, c_a = 1.4260 : x_s = -0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 7.0804 talairach xfm : /usr/local/freesurfer/subjects/05/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 -0.0000 131.3444 0.0000 -0.0000 1.0000 -126.5740 -0.0000 -1.0000 0.0000 135.0804 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 131.3444 0.0000 0.0000 -1.0000 135.0804 0.0000 1.0000 -0.0000 126.5740 -0.0000 -0.0000 -0.0000 1.0000 #-------------------------------------------- #@# Talairach Thu Sep 4 18:06:56 UTC 2025 /usr/local/freesurfer/subjects/05/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /opt/bin/bc /usr/local/freesurfer/subjects/05/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.4.1 Linux 702840b9e5e3 6.8.0-1017-gcp #19-Ubuntu SMP Tue Oct 15 19:02:59 UTC 2024 x86_64 GNU/Linux Thu Sep 4 18:06:56 UTC 2025 tmpdir is ./tmp.mri_nu_correct.mni.327 cd /usr/local/freesurfer/subjects/05/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.327/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_convert ./tmp.mri_nu_correct.mni.327/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.327/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from ./tmp.mri_nu_correct.mni.327/nu0.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -3.72529e-09) j_ras = (3.72529e-09, -7.45058e-09, -1) k_ras = (-1.18744e-08, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Thu Sep 4 18:11:08 UTC 2025 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... mv -f /usr/local/freesurfer/subjects/05/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /usr/local/freesurfer/subjects/05/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt Started at Thu Sep 4 18:11:08 UTC 2025 Ended at Thu Sep 4 18:11:37 UTC 2025 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox 7.4.1 --src: orig.mgz src image (geometry). --trg: /usr/local/freesurfer/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.03171 -0.13761 -0.04564 -1.07126; 0.09806 1.05200 0.42897 -10.23950; -0.02737 -0.46094 1.08192 2.10251; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. /usr/local/freesurfer/subjects/05/mri/transforms /usr/local/freesurfer/subjects/05/mri /usr/local/freesurfer/subjects/05/mri #-------------------------------------------- #@# Talairach Failure Detection Thu Sep 4 18:11:39 UTC 2025 /usr/local/freesurfer/subjects/05/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5379, pval=0.2115 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/05/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/05/mri/transforms/talairach_avi.log TalAviQA: 0.97564 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Sep 4 18:11:39 UTC 2025 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /opt/bin/bc /usr/local/freesurfer/subjects/05/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.4.1 Linux 702840b9e5e3 6.8.0-1017-gcp #19-Ubuntu SMP Tue Oct 15 19:02:59 UTC 2024 x86_64 GNU/Linux Thu Sep 4 18:11:39 UTC 2025 tmpdir is ./tmp.mri_nu_correct.mni.541 cd /usr/local/freesurfer/subjects/05/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.541/nu0.mgz --dtype uchar AntsN4BiasFieldCorrectionFs done mri_binarize --i ./tmp.mri_nu_correct.mni.541/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.541/ones.mgz 7.4.1 cwd /usr/local/freesurfer/subjects/05/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.541/nu0.mgz --min -1 --o ./tmp.mri_nu_correct.mni.541/ones.mgz sysname Linux hostname 702840b9e5e3 machine x86_64 user root input ./tmp.mri_nu_correct.mni.541/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.541/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Starting parallel 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Writing output to ./tmp.mri_nu_correct.mni.541/ones.mgz Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.541/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.541/input.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.541/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.541/input.mean.dat sysname Linux hostname 702840b9e5e3 machine x86_64 user root whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.541/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.541/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.541/ones.mgz --i ./tmp.mri_nu_correct.mni.541/nu0.mgz --sum ./tmp.mri_nu_correct.mni.541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.541/output.mean.dat 7.4.1 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.541/ones.mgz --i ./tmp.mri_nu_correct.mni.541/nu0.mgz --sum ./tmp.mri_nu_correct.mni.541/sum.junk --avgwf ./tmp.mri_nu_correct.mni.541/output.mean.dat sysname Linux hostname 702840b9e5e3 machine x86_64 user root whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.541/ones.mgz Loading ./tmp.mri_nu_correct.mni.541/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.541/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.541/nu0.mgz ./tmp.mri_nu_correct.mni.541/nu0.mgz mul 1.19508588345023867880 Saving result to './tmp.mri_nu_correct.mni.541/nu0.mgz' (type = MGH ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.541/nu0.mgz nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.541/nu0.mgz nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.541/nu0.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -3.72529e-09) j_ras = (3.72529e-09, -7.45058e-09, -1) k_ras = (-1.18744e-08, 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 7 seconds. FIRST_PERCENTILE 0.010000 WM_PERCENTILE 0.900000 MAX_R 50.000000 i1 = 5, i2 = 68 #mri_make_uchar# mapping 13 175 to 3 110 : b -5.97778 m 0.662157 : thresh 9.02774 maxsat 394.133 : nzero 12830671 nsat 0 Thu Sep 4 18:16:20 UTC 2025 mri_nu_correct.mni done mri_add_xform_to_header -c /usr/local/freesurfer/subjects/05/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz