What volume did the TF.label come from? Whatever it is, try adding --tkr-template volume.nii.gz
On 1/12/2023 9:12 PM, Shao-Min (Sean) Hung wrote:
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Sure.
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
DoLabelStatVol0
LabelCodeOffset0
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 dgreve@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 list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1tI61B-7G2xq2WwGF6AWryW_Fjx2KrG2DjExn0t9gs5MjWtEUFhytszRTe4QixYHFEjKKA-RuJuxf_AFCgAz4z3E027qVQnkLrBIB80GOBx6PdnvKb6mAYrZeEt57LH_SLJ5b49oMLXknnSvj1K6bJ3rLxr_4ZuQtuNwPw0tNo4wG4p2qhwjuYhSGNbCK8e3UNZbCCTaiUscDL0ReDPmsjM5R-7IV5dlPEseE_hS3c6kXNHDI5thYjxvzeeSsgr1GP2xP83qdA2e8GagKjMRaYfWbc4H_NSC1DXpIv0cbloulEfK1bPu6xXrlfJslqSyd/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.massgeneralbrigham.org/complianceline <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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