Try just one dash. Flair image needs to be provided with -flair <flair image>.
Here are explanation and examples of -T2, -FLAIR, -T2pial, -FLAIRpial flags:
“
T2 OR FLAIR TO IMPROVE PIAL SURFACES
Pial surfaces can be improved using the different contrast in T2 or FLAIR
images. The original pial surfaces without T2/FLAIR data are saved as
?h.woT2.pial or ?h.woFLAIR.pial, and new ?h.pial surfaces are created. One
example where this is useful is when there is dura in the brainmask.mgz that
isn't removed by skull stripping. The flags for these commands are:
-T2 <input T2 volume> or -FLAIR <input FLAIR volume>
(Specify the path to the T2 or FLAIR image to use)
-T2pial or -FLAIRpial
(Create new pial surfaces using T2 or FLAIR images)
An example of running a subject through Freesurfer with a T2 image is:
recon-all -s subjectname -i /path/to/input -T2 /path/to/T2_input -T2pial -all
T2 or FLAIR images can also be used with Freesurfer subjects that have already
been processed without them. Note that autorecon3 should also be re-ran to
compute statistics based on the new surfaces. For example:
recon-all -s subjectname -T2 /path/to/T2_volume -T2pial -autorecon3
“
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Alan Francis
Sent: Friday, September 1, 2023 5:11 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] T2 FLAIR Images
External Email - Use Caution
I tried the following command with the --flair flag but it did not work:
[DMK6P4G6FJ1G:~/SUBJECTS/NCANDA_S00033] alanfrancis% recon-all -s S00033 -i t1.nii.gz -i t2.nii.gz --flair -all
ERROR: Flag --flair unrecognized.
Could you please tell me where the --flair flag is slotted?
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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
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
mri_convert --flair t2.nii,gz 002.mgz
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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:
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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.
[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
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Alan N. Francis PhD
Assistant Professor of Neuroscience
Institute of Neuroscience
University of Texas, School of Medicine