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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
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:
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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
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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
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