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Good evening Doug et all:
I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: I opened the T2 image on Freeview. It looks normal. I tried running a second brain. Same problem. Appears normal on Freeview but recons wont run.
So I tried running the recons on the T1 alone and it ran without problems.
Thanks,
Alan
[DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/ fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n40000gq/T//tmp.W6p7a1 Mon Aug 7 16:06:21 CDT 2023
setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS cd /Users/alanfrancis/SUBJECTS /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n40000gq/T//tmp.W6p7a1 -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 /Applications/freesurfer/7.4.1/bin/fs-check-version
freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 pid 9192 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_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 /Users/alanfrancis/SUBJECTS Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 #-------------------------------------------- #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 Found 2 runs /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /Users/alanfrancis/SUBJECTS/NCANDA_S00042 \n mri_robust_template --mov /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz --average 1 --template /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt --subsample 200 --lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n 7.4.1
--mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz as movable/source volume. --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.4688, 0.4688, 0.6 size(0) = 0.9375, 0.9375, 1.2 *error: MultiRegistration::loadMovables: voxel size is different /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz.*
Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64
recon-all -s NCANDA_S00042 exited with ERRORS at Mon Aug 7 16:06:29 CDT 2023