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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
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 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 CautionDear 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 listFreesurfer@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_C0hv7qWJqtgttWDrBBLFEh5NY7xNJ... 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_Fjx2KrG2DjExn0t9gs5MjWt... < https://secure-web.cisco.com/1tI61B-7G2xq2WwGF6AWryW_Fjx2KrG2DjExn0t9gs5MjWt... .
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:
External Email - Use Caution
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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Hi Doug,
That solved the problem like a charm. By the way, the volume came from brain.mgz. Thank you!
Regards, Sean
On Sat, Jan 14, 2023 at 12:28 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
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:
External Email - Use CautionSure.
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 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 CautionDear 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 listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1zBobloczHVht4MzgegaTCRoLyStasjzYl9Jcy84A8W8AoT... 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
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-- 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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