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/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 > > <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 > 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 PhDAssistant Professor of NeuroscienceInstitute of Neuroscience* *University of Texas, School of Medicine* *Rio Grande Valley* *Texas.*
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