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Here's the command line: -- mri_label2vol --label /Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/Retinolabels/TF.label --temp /Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/004/fmc.nii.gz --reg /Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/register.dof6.lta --subject $subj --o /Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/Retinolabels/TS.nii -- Here's the terminal output: -- INFO: subject not needed, igorning. Number of labels: 1 /Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/Retinolabels/TF.label Annot File: (null) Template Volume: /Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/004/fmc.nii.gz Outut Volume: /Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/Retinolabels/TS.nii Registration File: /Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/register.dof6.lta Fill Threshold: 0 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: UNSTP041 Hemi: (null) UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects 7.1.1 Template RAS-to-Vox: -------- -0.28571 -0.00000 -0.00000 32.00000; -0.00000 -0.00000 -0.28571 32.00000; -0.00000 0.25000 -0.00000 17.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 49 nHits Thresh: 0 Loading registration from /Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/register.dof6.lta regio_read_register: loading lta RegMat: -------- 0.99970 0.02364 0.00603 -6.19680; -0.00433 -0.07116 0.99746 -14.83764; -0.02401 0.99718 0.07103 -9.81828; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- -0.28563 -0.00676 -0.00172 33.77051; 0.00686 -0.28491 -0.02029 34.80521; -0.00108 -0.01779 0.24936 13.29059; 0.00000 0.00000 0.00000 1.00000; nlabels = 1 Allocating Hit Volume (139264) voxels Loading /Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/Retinolabels/TF.label ERROR: label is not in tkreg coords so you need to specify atemplate with --tkr-template MRI. The MRI should be the volumethat the label was created on -- There was something I forgot to mention. I also suspect that the problem came from ROI creation. The ascii label column shows -1 for all coordinates. Thank you! Sean On Thu, Jan 12, 2023 at 11:29 PM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > Can you send your command line and full terminal output? > > On 1/8/2023 9:37 PM, Shao-Min (Sean) Hung wrote: > > External Email - Use Caution > Dear Doug, > > I have been having the following issue and haven't figured out a way to > get around it. I have also searched the archive and did not find > anything relevant enough to be helpful. > > The context is, I am drawing functional ROIs on volumetric data using > FreeView. After which, I use mri_label2vol to convert the label into a > volume for further analysis. > > I keep getting the following error: > > ERROR: label is not in tkreg coords so you need to specify atemplate with > --tkr-template MRI. The MRI should be the volumethat the label was created > on > > I used different templates to re-create the label but did not solve the > issue. Using a different template for mri_label2vol did not seem to help > either. I went back to check the labels, which seemed to be correctly drawn. > > Could you give me some directions to solve this issue? Thank you for your > help! > > Regards, > Sean > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1-swveHF7QEvcAPmj_C0hv7qWJqtgttWDrBBLFEh5NY7xNJ6sB-eDFDJVOPFQB2V5dVoIk3FugxWcHJgZAthTdQaFjM4Qr1hJaYjNUEfVtK5jh6Ztlx3HyBWrW-87ePDpYukcDUvFaVXi2fwkhcW8s8HHaEwD03eXt4Ykc1XtwOyMCArCMcluaMsRqwi3-uxWng4vw7X_NaR8QkcrpvV6crQvk74grkvo7JWYzN9FjUmsO0GJgFoJ_TLqUinfaPbjM7H-7MapvAYce94C2zSqUO9KcER7Y7SON2LwZjgeZCWYZIEX-EBX54OBkNdEOmYO/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/1tI61B-7G2xq2WwGF6AWryW_Fjx2KrG2DjExn0t9gs5MjWtEUFhytszRTe4QixYHFEjKKA-RuJuxf_AFCgAz4z3E027qVQnkLrBIB80GOBx6PdnvKb6mAYrZeEt57LH_SLJ5b49oMLXknnSvj1K6bJ3rLxr_4ZuQtuNwPw0tNo4wG4p2qhwjuYhSGNbCK8e3UNZbCCTaiUscDL0ReDPmsjM5R-7IV5dlPEseE_hS3c6kXNHDI5thYjxvzeeSsgr1GP2xP83qdA2e8GagKjMRaYfWbc4H_NSC1DXpIv0cbloulEfK1bPu6xXrlfJslqSyd/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1tI61B-7G2xq2WwGF6AWryW_Fjx2KrG2DjExn0t9gs5MjWtEUFhytszRTe4QixYHFEjKKA-RuJuxf_AFCgAz4z3E027qVQnkLrBIB80GOBx6PdnvKb6mAYrZeEt57LH_SLJ5b49oMLXknnSvj1K6bJ3rLxr_4ZuQtuNwPw0tNo4wG4p2qhwjuYhSGNbCK8e3UNZbCCTaiUscDL0ReDPmsjM5R-7IV5dlPEseE_hS3c6kXNHDI5thYjxvzeeSsgr1GP2xP83qdA2e8GagKjMRaYfWbc4H_NSC1DXpIv0cbloulEfK1bPu6xXrlfJslqSyd/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . > -- Shao-Min (Sean) Hung || Assistant Professor Faculty of Science and Engineering Waseda University ホン シャオミン 研究院講師 理工学術院 早稲田大学 My research at a glance <https://secure-web.cisco.com/1jy-dBGoMbHrnfMoW0bbt3ANCG1cx4FPClCKncNii9R8zKL5wEsCrfc-UVbVo8iHSpnI91RutJWdRxigeRzrM4lyIbvUR7fDXWwVc6GVJWSxhbUGUe8BzBlSCpisUrNRSSwbrRBIykzo_QQMe83E7nJfeuKJ73VPUq9HDmU5JETaFb9LjmFDm-LbjPd4mSNmE_Rx1P47pO9IRXIXB4DpChzAYLInekLmx5kgJlhKZYLiNwCRRdE2eZttruMuno16f1Y5WFx0sFdBLPImQt7K-8_GId8q3N_6JTtK_UjJGwdzI2bdu6XCw6BxCNrg6Q4fa/https%3A%2F%2Fkonaes.wixsite.com%2Fshao-min-hung>
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