External Email - Use Caution
Sorry, you need to pass it to recon-all with --flair or --T2
On 8/21/2023 1:19 PM, Alan Francis wrote:
External Email - Use Caution
Hi Doug:
Thanks for your reply. I am trying to set the T1.nii.gz as 001.mgz and
the T2.nii.gz as 002.mgz. So will the following command work?
mri_convert t2.nii.gz --flair 002.mgz
or is it:
mri_convert --flair t2.nii,gz 002.mgz
Thanks,
Alan
On Sun, Aug 20, 2023 at 4:17 PM Douglas N. Greve
<dgr...@mgh.harvard.edu> wrote:
External Email - Use Caution
How did you set up the T2? Did you set 001.mgz to be the T1 and
the 002.mgz to be the T2FLAIR? If so, that will not work. You
should pass the FLAIR with the --flair flag. recon-all will
register them together. Or do you just want to register them
outside of recon-all?
On 8/14/2023 2:46 PM, Alan Francis wrote:
External Email - Use Caution
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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--
/|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|/
/*
*Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience/
/University of Texas, School of Medicine/
/Rio Grande Valley
/
/Texas.
/
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