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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
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