External Email - Use Caution        

Thank you so much Yujing!

On Fri, Sep 1, 2023 at 5:45 PM Huang, Yujing <yhuan...@mgh.harvard.edu>
wrote:

>         External Email - Use Caution
>
> 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-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@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?
>
>
>
> thanks,
>
>
>
> Alan
>
>
>
> On Tue, Aug 22, 2023 at 9:08 AM Douglas N. Greve <dgr...@mgh.harvard.edu>
> wrote:
>
> *        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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> attempt from "secure-web.cisco.com" claiming to be*
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> <https://secure-web.cisco.com/1M20HEJzIvQQXRvjwrQnL4LteILxhvaPQvJhFfIZbci88mnwKaJWlX2CE2OpOEjuQTIMxgKETHa4OutI5Ko2qlTzT-xe6atP67QO_TJVtUN4qJ4tAvoIKMRpGgb7AeawzPFFtMrNA77Av5UwKTQexT3NUda7nZyko6AdFZNCaAbVNxbWvupdhQiohKs5DuwO7IitLIDmoZJZU72Cgv0k0pmOcb5sHwlHTvJGrzJT19Wbs9wIdGyiRYCS7SnT8AsM6lJ8RXAccNslnbjYAyL-eRPy4FYqoqCCUHz3FmbnfCfOMJL3YG-S4FEhIRj65mk5qlvAAo4KMmjU3c98_kbXmOg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
> <*MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/13NTeu_m-yMQSYHNYfh2etuLVvbt3wfde8sRVVn9bwAZRwaLtpw3wyH3JMG-Qz0CLXysdYcd55rXbIQtWz220NB7xrFSnNKnAaJGlVk0nO1Ja_soGI9wnn-V1aXjHhqW_KDX104CoSEGPcLzTuGop0BCMuQn5KXu4P3wdqjmtUtLE3PB58giMEfrFhy__DBczq9QPWLgx7BuenPOzNfwkAj6c865APTddzFcWcE-xZe0EQyTF_c-U-ETaJZkQbdJfWjO6CyQppeJSiMPzaYKIHCmmxDkMf-ULfQnyPoCwmCwi4q6HELUdO01rH6aALXPktGO9qgSn9LKRzUkkthBZCA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
> <https://secure-web.cisco.com/1M20HEJzIvQQXRvjwrQnL4LteILxhvaPQvJhFfIZbci88mnwKaJWlX2CE2OpOEjuQTIMxgKETHa4OutI5Ko2qlTzT-xe6atP67QO_TJVtUN4qJ4tAvoIKMRpGgb7AeawzPFFtMrNA77Av5UwKTQexT3NUda7nZyko6AdFZNCaAbVNxbWvupdhQiohKs5DuwO7IitLIDmoZJZU72Cgv0k0pmOcb5sHwlHTvJGrzJT19Wbs9wIdGyiRYCS7SnT8AsM6lJ8RXAccNslnbjYAyL-eRPy4FYqoqCCUHz3FmbnfCfOMJL3YG-S4FEhIRj65mk5qlvAAo4KMmjU3c98_kbXmOg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>>
> .
>
>
>
> --
>
> *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*
>
>
>
>
> *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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>  <
> https://secure-web.cisco.com/13NTeu_m-yMQSYHNYfh2etuLVvbt3wfde8sRVVn9bwAZRwaLtpw3wyH3JMG-Qz0CLXysdYcd55rXbIQtWz220NB7xrFSnNKnAaJGlVk0nO1Ja_soGI9wnn-V1aXjHhqW_KDX104CoSEGPcLzTuGop0BCMuQn5KXu4P3wdqjmtUtLE3PB58giMEfrFhy__DBczq9QPWLgx7BuenPOzNfwkAj6c865APTddzFcWcE-xZe0EQyTF_c-U-ETaJZkQbdJfWjO6CyQppeJSiMPzaYKIHCmmxDkMf-ULfQnyPoCwmCwi4q6HELUdO01rH6aALXPktGO9qgSn9LKRzUkkthBZCA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
>


-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*
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