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 >> >> _______________________________________________ >> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1tfx-v6p83VIo_MZpzoizjCoJYy4dDGj1CSBl3Nxq8pBNrj3V39y8Wot8aUiQ8gp4LAfkHCRoWJWaK4cKGZmZ1yQkmf-enBHe5fQjNIzn-rJSOoVHBbKTQ5MHzGwfMJ063pgGOe4C0tCTiLnUMtudINTznxa46IJduJT9RPhPb8HBkFz9sgvhTdWxZm9ai1BCDowCQ6-lUnOhIJtf1QFkFjMvF2WYgnTV9obWEV5bW7u9XVx8ohNvmDq3tnbjtu22Gj4Qa8O54lJnQW63Npr5yMOPZ9zzcnOPOF4ZZfjHpVPzSymteQAqPTRQLoZBbX5Up63_n1l8Fmz19RlH5cofGA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/11uouOsdwrMdQflnYEnhqplXN8xNdR13TfmPAve-47rXjsF6yz6aRASVm8M4X2LMc2TkoYtxuFL2YDngD1Oi256obLXHkJ24-nqSVjTYkcBYSJraZkz_LSnJLlUbyi78ZqwsCYFAfVLYe4Jaih9PN5Gymp78vlM8KW2QmGJOJq3DVPDg0hU0s2_OgqDaaoYM2kxYkzfd5Yvk_hRo0c0G5s-x8JKb7dagkGCB6N7f1F7D8_WUy7nZpSptKL5B7z5iQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1tfx-v6p83VIo_MZpzoizjCoJYy4dDGj1CSBl3Nxq8pBNrj3V39y8Wot8aUiQ8gp4LAfkHCRoWJWaK4cKGZmZ1yQkmf-enBHe5fQjNIzn-rJSOoVHBbKTQ5MHzGwfMJ063pgGOe4C0tCTiLnUMtudINTznxa46IJduJT9RPhPb8HBkFz9sgvhTdWxZm9ai1BCDowCQ6-lUnOhIJtf1QFkFjMvF2WYgnTV9obWEV5bW7u9XVx8ohNvmDq3tnbjtu22Gj4Qa8O54lJnQW63Npr5yMOPZ9zzcnOPOF4ZZfjHpVPzSymteQAqPTRQLoZBbX5Up63_n1l8Fmz19RlH5cofGA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <https://secure-web.cisco.com/1hnUd6Nc-S0Q-j_PocjKu7mWlKgWdU0mKPIwdFpDRyzAI8-0ZGCHCyyxhQk_SbFM8se1MYTquaZY9imPbgniTjNkSXHyWJX9T_lqE2AmldPS6Kyu5GGnBaL8Jb4ELHBPQksGyR0UdbaIeVND3r_JkJ4MU-G6bv5miNstJo7Xoc8PLiGfNlDVT_mkx7LrFQMecrkt-ZIbbGvOcv-DOoQuTXBoDwuCXBtsbADwYeP-VTd1D9745omQmORBbItcVsKzteK1tC1jGIt3n8UZuVp3CluZQWguK2QCi99tdx5EOGO2mtdnn0aS_L7DckyS4u4_8rWo2SxR5JVGJL234pIjtHg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >> The information in this e-mail is intended only for the person to whom it >> is addressed. 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Francis PhD Assistant Professor of Neuroscience Institute of > Neuroscience* > *University of Texas, School of Medicine* > > *Rio Grande Valley * > > *Texas. * > > > > _______________________________________________ > Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has > detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1tfx-v6p83VIo_MZpzoizjCoJYy4dDGj1CSBl3Nxq8pBNrj3V39y8Wot8aUiQ8gp4LAfkHCRoWJWaK4cKGZmZ1yQkmf-enBHe5fQjNIzn-rJSOoVHBbKTQ5MHzGwfMJ063pgGOe4C0tCTiLnUMtudINTznxa46IJduJT9RPhPb8HBkFz9sgvhTdWxZm9ai1BCDowCQ6-lUnOhIJtf1QFkFjMvF2WYgnTV9obWEV5bW7u9XVx8ohNvmDq3tnbjtu22Gj4Qa8O54lJnQW63Npr5yMOPZ9zzcnOPOF4ZZfjHpVPzSymteQAqPTRQLoZBbX5Up63_n1l8Fmz19RlH5cofGA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <https://secure-web.cisco.com/1jpNNfpShxvmgjaYJtjtm6lkl2SMs88sphH8hlxJybMbUdk8BJf7C_IpCVkiCTvvhlsYpoumYQKJU6Om3Fsc_sm_zwJcqBfNMjvN_fGl9XrnE6s9sqpyQE-Tj6EjMA7woX--Eb854P6cCmIGvgySnTouENN6rAVE60HvHlDl-N_QyPCKGtAkeugxjByAxwTQuMVUaL9jhTNVPZZom6DrhWXrlRr4uUwQ76TSc3oU9x724psphMbKrWTkNtcnEoxFNHIEQMxCfDWN5AAvu0_un2w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1tfx-v6p83VIo_MZpzoizjCoJYy4dDGj1CSBl3Nxq8pBNrj3V39y8Wot8aUiQ8gp4LAfkHCRoWJWaK4cKGZmZ1yQkmf-enBHe5fQjNIzn-rJSOoVHBbKTQ5MHzGwfMJ063pgGOe4C0tCTiLnUMtudINTznxa46IJduJT9RPhPb8HBkFz9sgvhTdWxZm9ai1BCDowCQ6-lUnOhIJtf1QFkFjMvF2WYgnTV9obWEV5bW7u9XVx8ohNvmDq3tnbjtu22Gj4Qa8O54lJnQW63Npr5yMOPZ9zzcnOPOF4ZZfjHpVPzSymteQAqPTRQLoZBbX5Up63_n1l8Fmz19RlH5cofGA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1M20HEJzIvQQXRvjwrQnL4LteILxhvaPQvJhFfIZbci88mnwKaJWlX2CE2OpOEjuQTIMxgKETHa4OutI5Ko2qlTzT-xe6atP67QO_TJVtUN4qJ4tAvoIKMRpGgb7AeawzPFFtMrNA77Av5UwKTQexT3NUda7nZyko6AdFZNCaAbVNxbWvupdhQiohKs5DuwO7IitLIDmoZJZU72Cgv0k0pmOcb5sHwlHTvJGrzJT19Wbs9wIdGyiRYCS7SnT8AsM6lJ8RXAccNslnbjYAyL-eRPy4FYqoqCCUHz3FmbnfCfOMJL3YG-S4FEhIRj65mk5qlvAAo4KMmjU3c98_kbXmOg/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 PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*
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