- This topic has 11 replies, 2 voices, and was last updated 5 years ago by Anand Joshi.
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September 11, 2019 at 11:29 pm #1882amysore3Participant
As I run the SV-registration module on an MRI scan, the entire process completes without any error and I can see the resulting volumes in the lower right hand corner display as they are being computed. When I try to access the labeled volume (File-Open-Label volume…), I am unable to find all the labeled volumes saved in the folder or access them in any other way. Are my labeled volumes not getting saved? If yes, why? How can I change it to save and access my labeled volumes? Please provide suggestions in this regard. Any help will be appreciated. Thank you in advance!
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September 17, 2019 at 11:18 am #1883Anand JoshiModerator
Hi, The labeled volume should be automatically stored in the same directory as the MRI scan. They have filenames <subjectid>.svreg.label.nii.gz
Are you able to find that file?
Here is the list of output files
http://brainsuite.org/processing/svreg/output/Please let me know if you find these files generated in your mri directory.
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September 18, 2019 at 8:43 am #1913amysore3Participant
Thank you for the response but I am not able to see these files in the same directory as my MRI scan. It feels like they aren’t getting saved. But I am not getting any error either which I believe means that the SVreg is running successfully but isn’t saving the labelled volumes. Please let me know what I could.
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September 18, 2019 at 10:01 am #1914Anand JoshiModerator
What are the files do you see in the mri directory? Do you have the .dfs files there?
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September 18, 2019 at 11:05 am #1915amysore3Participant
Yes, I do see all the .dfs files in the MRI directory
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September 18, 2019 at 11:09 am #1916amysore3Participant
I see only “.hemi.label.nii.gz”, “.pvc.label.nii.gz” and “.skull.label.nii.gz” labelled volumes and I see all the .dfs files.
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September 18, 2019 at 11:27 am #1917Anand JoshiModerator
Are there any files with svreg extension (e.g. *.svreg.dfs)
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September 18, 2019 at 11:31 am #1918amysore3Participant
Yes., there are about 8-10 files with .svreg.dfs.
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September 18, 2019 at 12:03 pm #1919Anand JoshiModerator
That means svreg has finished, however perhaps only the surface registration has run.
Please make sure that the ‘surface registration only’ box us unchecked.
http://brainsuite.org/quickstart/svreg/ -
September 18, 2019 at 12:12 pm #1920amysore3Participant
Thank you. I will try running it again.
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September 18, 2019 at 1:54 pm #1921amysore3Participant
That worked. Thank you!
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September 18, 2019 at 1:57 pm #1922Anand JoshiModerator
Awesome!
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